From e95c60c428670eabbae29f4525ea58cbf37ff2b7 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 11 Nov 2024 09:26:46 -0500 Subject: [PATCH 01/12] Change T1wACPC to ACPC and T1wNative to anat. --- .circleci/DSCSDSI_outputs.txt | 14 +++---- .circleci/DSDTI_nofmap_outputs.txt | 14 +++---- .circleci/DSDTI_outputs.txt | 14 +++---- .circleci/DSDTI_synsdc_outputs.txt | 14 +++---- .circleci/IntramodalTemplate_outputs.txt | 28 +++++++------- .circleci/get_data.sh | 32 ++++++++-------- qsiprep/interfaces/reports.py | 10 ++--- qsiprep/tests/data/drbuddi_rpe_outputs.txt | 18 ++++----- .../data/drbuddi_shoreline_epi_outputs.txt | 18 ++++----- .../data/drbuddi_tensorline_epi_outputs.txt | 18 ++++----- qsiprep/tests/data/dscsdsi_outputs.txt | 28 +++++++------- qsiprep/tests/data/dsdti_nofmap_outputs.txt | 28 +++++++------- qsiprep/tests/data/dsdti_synfmap_outputs.txt | 28 +++++++------- qsiprep/tests/data/dsdti_topup_outputs.txt | 28 +++++++------- qsiprep/tests/data/forrest_gump_outputs.txt | 28 +++++++------- .../data/intramodal_template_outputs.txt | 38 +++++++++---------- .../data/maternal_brain_project_outputs.txt | 28 +++++++------- qsiprep/workflows/anatomical/volume.py | 12 +++--- qsiprep/workflows/dwi/derivatives.py | 20 +++++----- qsiprep/workflows/dwi/finalize.py | 2 +- 20 files changed, 210 insertions(+), 210 deletions(-) diff --git a/.circleci/DSCSDSI_outputs.txt b/.circleci/DSCSDSI_outputs.txt index 7fbf76ba..51f67c70 100644 --- a/.circleci/DSCSDSI_outputs.txt +++ b/.circleci/DSCSDSI_outputs.txt @@ -26,13 +26,13 @@ qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_confounds.tsv qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_desc-ImageQC_dwi.csv qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_desc-SliceQC_dwi.json qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_dwiqc.json -qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-3dSHORE_cnr.nii.gz -qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-brain_mask.nii.gz -qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.b -qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.bval -qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.bvec -qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.nii.gz -qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_dwiref.nii.gz +qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-3dSHORE_cnr.nii.gz +qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-brain_mask.nii.gz +qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b +qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bval +qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bvec +qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.nii.gz +qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_dwiref.nii.gz qsiprep/sub-tester/figures qsiprep/sub-tester/figures/sub-tester_acq-HASC55AP_carpetplot.svg qsiprep/sub-tester/figures/sub-tester_acq-HASC55AP_coreg.svg diff --git a/.circleci/DSDTI_nofmap_outputs.txt b/.circleci/DSDTI_nofmap_outputs.txt index ef61321f..7c5eb983 100644 --- a/.circleci/DSDTI_nofmap_outputs.txt +++ b/.circleci/DSDTI_nofmap_outputs.txt @@ -26,13 +26,13 @@ qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_dwiqc.json -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-brain_mask.nii.gz -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-eddy_cnr.nii.gz -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bval -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bvec -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.nii.gz -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwiref.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz qsiprep/sub-PNC/figures qsiprep/sub-PNC/figures/sub-PNC_acq-realistic_carpetplot.svg qsiprep/sub-PNC/figures/sub-PNC_acq-realistic_coreg.svg diff --git a/.circleci/DSDTI_outputs.txt b/.circleci/DSDTI_outputs.txt index daf11d1f..cad7326d 100644 --- a/.circleci/DSDTI_outputs.txt +++ b/.circleci/DSDTI_outputs.txt @@ -26,13 +26,13 @@ qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_dwiqc.json -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-brain_mask.nii.gz -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-eddy_cnr.nii.gz -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bval -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bvec -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.nii.gz -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwiref.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz qsiprep/sub-PNC/figures qsiprep/sub-PNC/figures/sub-PNC_acq-realistic_carpetplot.svg qsiprep/sub-PNC/figures/sub-PNC_acq-realistic_coreg.svg diff --git a/.circleci/DSDTI_synsdc_outputs.txt b/.circleci/DSDTI_synsdc_outputs.txt index ea6501fd..bac25180 100644 --- a/.circleci/DSDTI_synsdc_outputs.txt +++ b/.circleci/DSDTI_synsdc_outputs.txt @@ -26,13 +26,13 @@ qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_dwiqc.json -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-brain_mask.nii.gz -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-eddy_cnr.nii.gz -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bval -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bvec -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.nii.gz -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwiref.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz qsiprep/sub-PNC/figures qsiprep/sub-PNC/figures/sub-PNC_acq-realistic_carpetplot.svg qsiprep/sub-PNC/figures/sub-PNC_acq-realistic_coreg.svg diff --git a/.circleci/IntramodalTemplate_outputs.txt b/.circleci/IntramodalTemplate_outputs.txt index 020a87bb..85579125 100644 --- a/.circleci/IntramodalTemplate_outputs.txt +++ b/.circleci/IntramodalTemplate_outputs.txt @@ -45,24 +45,24 @@ qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_confounds.tsv qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_desc-ImageQC_dwi.csv qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_desc-SliceQC_dwi.json qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_dwiqc.json -qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-brain_mask.nii.gz -qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-none_cnr.nii.gz -qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.b -qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.bval -qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.bvec -qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.nii.gz -qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_dwiref.nii.gz +qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-brain_mask.nii.gz +qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-none_cnr.nii.gz +qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.b +qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.bval +qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.bvec +qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.nii.gz +qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_dwiref.nii.gz qsiprep/sub-tester/ses-2 qsiprep/sub-tester/ses-2/dwi qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_confounds.tsv qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_desc-ImageQC_dwi.csv qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_desc-SliceQC_dwi.json qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_dwiqc.json -qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-brain_mask.nii.gz -qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-none_cnr.nii.gz -qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.b -qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.bval -qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.bvec -qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.nii.gz -qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_dwiref.nii.gz +qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-brain_mask.nii.gz +qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-none_cnr.nii.gz +qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b +qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bval +qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bvec +qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.nii.gz +qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_dwiref.nii.gz /tmp/twoses/derivatives diff --git a/.circleci/get_data.sh b/.circleci/get_data.sh index c5a972ef..a66e1eb2 100644 --- a/.circleci/get_data.sh +++ b/.circleci/get_data.sh @@ -290,14 +290,14 @@ Contents: - data/multishell_output/qsiprep/sub-ABCD/anat/sub-ABCD_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz - data/multishell_output/qsiprep/sub-ABCD/anat/sub-ABCD_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_confounds.tsv - - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_b0series.nii.gz - - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-brain_mask.nii.gz - - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-eddy_cnr.nii.gz - - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwi.b - - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwi.bval - - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwi.bvec - - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwi.nii.gz - - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwiref.nii.gz + - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-ACPC_b0series.nii.gz + - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-ACPC_desc-brain_mask.nii.gz + - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-ACPC_desc-eddy_cnr.nii.gz + - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-ACPC_desc-preproc_dwi.b + - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-ACPC_desc-preproc_dwi.bval + - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-ACPC_desc-preproc_dwi.bvec + - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-ACPC_desc-preproc_dwi.nii.gz + - data/multishell_output/qsiprep/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-ACPC_dwiref.nii.gz singleshell_output: @@ -328,14 +328,14 @@ Contents: - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv - - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_b0series.nii.gz - - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-brain_mask.nii.gz - - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-eddy_cnr.nii.gz - - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b - - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bval - - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bvec - - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.nii.gz - - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwiref.nii.gz + - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_b0series.nii.gz + - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz + - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz + - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b + - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval + - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec + - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz + - data/singleshell_output/qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz - data/singleshell_output/qsiprep/sub-PNC/figures/sub-PNC_acq-realistic_carpetplot.svg - data/singleshell_output/qsiprep/sub-PNC/figures/sub-PNC_acq-realistic_coreg.svg - data/singleshell_output/qsiprep/sub-PNC/figures/sub-PNC_acq-realistic_desc-sdc_b0.svg diff --git a/qsiprep/interfaces/reports.py b/qsiprep/interfaces/reports.py index a7c90453..9e548c46 100644 --- a/qsiprep/interfaces/reports.py +++ b/qsiprep/interfaces/reports.py @@ -44,7 +44,7 @@ \t\t
  • Structural images: {n_t1s:d} T1-weighted {t2w}
    • \t\t
  • Diffusion-weighted series: inputs {n_dwis:d}, outputs {n_outputs:d}
    • {groupings} -\t\t
  • Resampling targets: T1wACPC
    • +\t\t
  • Resampling targets: ACPC
    • \t\t
  • Transform targets: {output_spaces}
    • \t """ @@ -55,7 +55,7 @@ \t\t
  • Structural images: {n_t1s:d} T1-weighted {t2w}
    • \t\t
  • Diffusion-weighted series: inputs {n_dwis:d}, outputs {n_outputs:d}
    • {groupings} -\t\t
  • Resampling targets: T1wACPC +\t\t
  • Resampling targets: ACPC
    • \t """ @@ -68,7 +68,7 @@ \t\t\t
  • Denoising Window: {denoise_window}
    • \t\t\t
  • HMC Transform: {hmc_transform}
    • \t\t\t
  • HMC Model: {hmc_model}
    • -\t\t\t
  • DWI series resampled to spaces: T1wACPC
    • +\t\t\t
  • DWI series resampled to spaces: ACPC
    • \t\t\t
  • Confounds collected: {confounds}
    • \t\t\t
  • Impute slice threshold: {impute_slice_threshold}
    • \t\t @@ -207,7 +207,7 @@ def _generate_segment(self): n_dwis=n_dwis, n_outputs=n_outputs, groupings=groupings, - output_spaces=["T1wACPC", self.inputs.template], + output_spaces=["ACPC", self.inputs.template], ) @@ -261,7 +261,7 @@ def _generate_segment(self): hmc_model=self.inputs.hmc_model, denoise_method=self.inputs.denoise_method, denoise_window=self.inputs.dwi_denoise_window, - output_spaces="T1wACPC", + output_spaces="ACPC", confounds=re.sub(r"[\t ]+", ", ", conflist), impute_slice_threshold=self.inputs.impute_slice_threshold, validation_reports=validation_summary, diff --git a/qsiprep/tests/data/drbuddi_rpe_outputs.txt b/qsiprep/tests/data/drbuddi_rpe_outputs.txt index 9aa70f94..ce6749bc 100644 --- a/qsiprep/tests/data/drbuddi_rpe_outputs.txt +++ b/qsiprep/tests/data/drbuddi_rpe_outputs.txt @@ -10,12 +10,12 @@ sub-tinytensors/dwi sub-tinytensors/dwi/sub-tinytensors_confounds.tsv sub-tinytensors/dwi/sub-tinytensors_desc-ImageQC_dwi.csv sub-tinytensors/dwi/sub-tinytensors_desc-SliceQC_dwi.json -sub-tinytensors/dwi/sub-tinytensors_space-T1w_desc-brain_mask.nii.gz -sub-tinytensors/dwi/sub-tinytensors_space-T1w_desc-eddy_cnr.nii.gz -sub-tinytensors/dwi/sub-tinytensors_space-T1w_desc-preproc_dwi.b -sub-tinytensors/dwi/sub-tinytensors_space-T1w_desc-preproc_dwi.bval -sub-tinytensors/dwi/sub-tinytensors_space-T1w_desc-preproc_dwi.bvec -sub-tinytensors/dwi/sub-tinytensors_space-T1w_desc-preproc_dwi.nii.gz -sub-tinytensors/dwi/sub-tinytensors_space-T1w_desc-preproc_dwi.json -sub-tinytensors/dwi/sub-tinytensors_space-T1w_desc-preproc_dwi.b_table.txt -sub-tinytensors/dwi/sub-tinytensors_space-T1w_dwiref.nii.gz +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-brain_mask.nii.gz +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-eddy_cnr.nii.gz +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.b +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.bval +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.bvec +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.nii.gz +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.json +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.b_table.txt +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt b/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt index 847a57a6..3e728570 100644 --- a/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt +++ b/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt @@ -10,12 +10,12 @@ sub-tinytensors/dwi sub-tinytensors/dwi/sub-tinytensors_dir-PA_confounds.tsv sub-tinytensors/dwi/sub-tinytensors_dir-PA_desc-ImageQC_dwi.csv sub-tinytensors/dwi/sub-tinytensors_dir-PA_desc-SliceQC_dwi.json -sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-T1w_desc-brain_mask.nii.gz -sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-T1w_desc-none_cnr.nii.gz -sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-T1w_desc-preproc_dwi.b -sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-T1w_desc-preproc_dwi.bval -sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-T1w_desc-preproc_dwi.bvec -sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-T1w_desc-preproc_dwi.nii.gz -sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-T1w_desc-preproc_dwi.json -sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-T1w_desc-preproc_dwi.b_table.txt -sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-T1w_dwiref.nii.gz +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-brain_mask.nii.gz +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-none_cnr.nii.gz +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.b +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.bval +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.bvec +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.nii.gz +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.json +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.b_table.txt +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt b/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt index 3503965b..1bb1cb0e 100644 --- a/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt +++ b/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt @@ -10,12 +10,12 @@ sub-PNC/dwi sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-brain_mask.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bval -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bvec -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b_table.txt -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-tensor_cnr.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwiref.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-tensor_cnr.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/dscsdsi_outputs.txt b/qsiprep/tests/data/dscsdsi_outputs.txt index b5d06ea3..a8b135e9 100644 --- a/qsiprep/tests/data/dscsdsi_outputs.txt +++ b/qsiprep/tests/data/dscsdsi_outputs.txt @@ -12,21 +12,21 @@ sub-tester/anat/sub-tester_desc-brain_mask.nii.gz sub-tester/anat/sub-tester_desc-preproc_T1w.json sub-tester/anat/sub-tester_desc-preproc_T1w.nii.gz sub-tester/anat/sub-tester_dseg.nii.gz -sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -sub-tester/anat/sub-tester_from-T1wACPC_to-T1wNative_mode-image_xfm.mat -sub-tester/anat/sub-tester_from-T1wNative_to-T1wACPC_mode-image_xfm.mat -sub-tester/anat/sub-tester_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -sub-tester/anat/sub-tester_from-orig_to-T1w_mode-image_xfm.txt +sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-tester/anat/sub-tester_from-ACPC_to-anat_mode-image_xfm.mat +sub-tester/anat/sub-tester_from-anat_to-ACPC_mode-image_xfm.mat +sub-tester/anat/sub-tester_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-tester/anat/sub-tester_from-orig_to-anat_mode-image_xfm.txt sub-tester/dwi sub-tester/dwi/sub-tester_acq-HASC55AP_confounds.tsv sub-tester/dwi/sub-tester_acq-HASC55AP_desc-ImageQC_dwi.csv sub-tester/dwi/sub-tester_acq-HASC55AP_desc-SliceQC_dwi.json -sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-3dSHORE_cnr.nii.gz -sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-brain_mask.nii.gz -sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.b -sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.bval -sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.bvec -sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.nii.gz -sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.json -sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.b_table.txt -sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_dwiref.nii.gz +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-3dSHORE_cnr.nii.gz +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-brain_mask.nii.gz +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bval +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bvec +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.nii.gz +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.json +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b_table.txt +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/dsdti_nofmap_outputs.txt b/qsiprep/tests/data/dsdti_nofmap_outputs.txt index b60f6e93..d8c690d7 100644 --- a/qsiprep/tests/data/dsdti_nofmap_outputs.txt +++ b/qsiprep/tests/data/dsdti_nofmap_outputs.txt @@ -12,21 +12,21 @@ sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz sub-PNC/anat/sub-PNC_desc-preproc_T1w.json sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz sub-PNC/anat/sub-PNC_dseg.nii.gz -sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-T1wACPC_to-T1wNative_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-T1wNative_to-T1wACPC_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-orig_to-T1w_mode-image_xfm.txt +sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-orig_to-anat_mode-image_xfm.txt sub-PNC/dwi sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-brain_mask.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-eddy_cnr.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bval -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bvec -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b_table.txt -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwiref.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/dsdti_synfmap_outputs.txt b/qsiprep/tests/data/dsdti_synfmap_outputs.txt index b60f6e93..d8c690d7 100644 --- a/qsiprep/tests/data/dsdti_synfmap_outputs.txt +++ b/qsiprep/tests/data/dsdti_synfmap_outputs.txt @@ -12,21 +12,21 @@ sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz sub-PNC/anat/sub-PNC_desc-preproc_T1w.json sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz sub-PNC/anat/sub-PNC_dseg.nii.gz -sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-T1wACPC_to-T1wNative_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-T1wNative_to-T1wACPC_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-orig_to-T1w_mode-image_xfm.txt +sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-orig_to-anat_mode-image_xfm.txt sub-PNC/dwi sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-brain_mask.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-eddy_cnr.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bval -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bvec -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b_table.txt -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwiref.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/dsdti_topup_outputs.txt b/qsiprep/tests/data/dsdti_topup_outputs.txt index b60f6e93..d8c690d7 100644 --- a/qsiprep/tests/data/dsdti_topup_outputs.txt +++ b/qsiprep/tests/data/dsdti_topup_outputs.txt @@ -12,21 +12,21 @@ sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz sub-PNC/anat/sub-PNC_desc-preproc_T1w.json sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz sub-PNC/anat/sub-PNC_dseg.nii.gz -sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-T1wACPC_to-T1wNative_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-T1wNative_to-T1wACPC_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-orig_to-T1w_mode-image_xfm.txt +sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-orig_to-anat_mode-image_xfm.txt sub-PNC/dwi sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-brain_mask.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-eddy_cnr.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bval -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bvec -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.nii.gz -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b_table.txt -sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwiref.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/forrest_gump_outputs.txt b/qsiprep/tests/data/forrest_gump_outputs.txt index b3223a7c..9733a1b5 100644 --- a/qsiprep/tests/data/forrest_gump_outputs.txt +++ b/qsiprep/tests/data/forrest_gump_outputs.txt @@ -12,23 +12,23 @@ sub-01/anat/sub-01_desc-brain_mask.nii.gz sub-01/anat/sub-01_desc-preproc_T1w.json sub-01/anat/sub-01_desc-preproc_T1w.nii.gz sub-01/anat/sub-01_dseg.nii.gz -sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -sub-01/anat/sub-01_from-T1wACPC_to-T1wNative_mode-image_xfm.mat -sub-01/anat/sub-01_from-T1wNative_to-T1wACPC_mode-image_xfm.mat -sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-01/anat/sub-01_from-ACPC_to-anat_mode-image_xfm.mat +sub-01/anat/sub-01_from-anat_to-ACPC_mode-image_xfm.mat +sub-01/anat/sub-01_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 sub-01/ses-forrestgump sub-01/ses-forrestgump/anat -sub-01/ses-forrestgump/anat/sub-01_ses-forrestgump_rec-autobox_from-orig_to-T1w_mode-image_xfm.txt +sub-01/ses-forrestgump/anat/sub-01_ses-forrestgump_rec-autobox_from-orig_to-anat_mode-image_xfm.txt sub-01/ses-forrestgump/dwi sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_confounds.tsv sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_desc-ImageQC_dwi.csv sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_desc-SliceQC_dwi.json -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-T1w_desc-brain_mask.nii.gz -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-T1w_desc-eddy_cnr.nii.gz -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-T1w_desc-preproc_dwi.b -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-T1w_desc-preproc_dwi.bval -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-T1w_desc-preproc_dwi.bvec -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-T1w_desc-preproc_dwi.nii.gz -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-T1w_desc-preproc_dwi.json -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-T1w_desc-preproc_dwi.b_table.txt -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-T1w_dwiref.nii.gz +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-brain_mask.nii.gz +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-eddy_cnr.nii.gz +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.b +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.bval +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.bvec +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.nii.gz +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.json +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.b_table.txt +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/intramodal_template_outputs.txt b/qsiprep/tests/data/intramodal_template_outputs.txt index e3bede5d..f2a2bc8d 100644 --- a/qsiprep/tests/data/intramodal_template_outputs.txt +++ b/qsiprep/tests/data/intramodal_template_outputs.txt @@ -10,8 +10,8 @@ sub-tester/anat sub-tester/anat/sub-tester_desc-brain_mask.nii.gz sub-tester/anat/sub-tester_desc-preproc_T1w.nii.gz sub-tester/anat/sub-tester_dseg.nii.gz -sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -sub-tester/anat/sub-tester_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-tester/anat/sub-tester_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 sub-tester/anat/sub-tester_label-CSF_probseg.nii.gz sub-tester/anat/sub-tester_label-GM_probseg.nii.gz sub-tester/anat/sub-tester_label-WM_probseg.nii.gz @@ -39,29 +39,29 @@ sub-tester/figures/sub-tester_ses-2_acq-HASC55AP_tointramodal.svg sub-tester/figures/sub-tester_t1_2_mni.svg sub-tester/ses-1 sub-tester/ses-1/anat -sub-tester/ses-1/anat/sub-tester_ses-1_from-orig_to-T1w_mode-image_xfm.txt +sub-tester/ses-1/anat/sub-tester_ses-1_from-orig_to-anat_mode-image_xfm.txt sub-tester/ses-1/dwi sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_confounds.tsv sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_desc-ImageQC_dwi.csv sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_desc-SliceQC_dwi.json -sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-brain_mask.nii.gz -sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-none_cnr.nii.gz -sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.b -sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.bval -sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.bvec -sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.nii.gz -sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.json -sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_dwiref.nii.gz +sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-brain_mask.nii.gz +sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-none_cnr.nii.gz +sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.b +sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.bval +sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.bvec +sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.nii.gz +sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.json +sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_dwiref.nii.gz sub-tester/ses-2 sub-tester/ses-2/dwi sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_confounds.tsv sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_desc-ImageQC_dwi.csv sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_desc-SliceQC_dwi.json -sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-brain_mask.nii.gz -sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-none_cnr.nii.gz -sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.b -sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.bval -sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.bvec -sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.nii.gz -sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.json -sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_dwiref.nii.gz +sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-brain_mask.nii.gz +sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-none_cnr.nii.gz +sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b +sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bval +sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bvec +sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.nii.gz +sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.json +sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/maternal_brain_project_outputs.txt b/qsiprep/tests/data/maternal_brain_project_outputs.txt index 73ce1005..3878e4e0 100644 --- a/qsiprep/tests/data/maternal_brain_project_outputs.txt +++ b/qsiprep/tests/data/maternal_brain_project_outputs.txt @@ -12,24 +12,24 @@ sub-01/anat/sub-01_desc-brain_mask.nii.gz sub-01/anat/sub-01_desc-preproc_T1w.json sub-01/anat/sub-01_desc-preproc_T1w.nii.gz sub-01/anat/sub-01_dseg.nii.gz -sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -sub-01/anat/sub-01_from-T1wACPC_to-T1wNative_mode-image_xfm.mat -sub-01/anat/sub-01_from-T1wNative_to-T1wACPC_mode-image_xfm.mat -sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-01/anat/sub-01_from-ACPC_to-anat_mode-image_xfm.mat +sub-01/anat/sub-01_from-anat_to-ACPC_mode-image_xfm.mat +sub-01/anat/sub-01_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 sub-01/ses-01 sub-01/ses-01/anat -sub-01/ses-01/anat/sub-01_ses-01_rec-autobox_from-orig_to-T1w_mode-image_xfm.txt +sub-01/ses-01/anat/sub-01_ses-01_rec-autobox_from-orig_to-anat_mode-image_xfm.txt sub-01/ses-01/dwi sub-01/ses-01/dwi/sub-01_ses-01_confounds.tsv sub-01/ses-01/dwi/sub-01_ses-01_desc-ImageQC_dwi.csv sub-01/ses-01/dwi/sub-01_ses-01_desc-SliceQC_dwi.json sub-01/ses-01/dwi/sub-01_ses-01_hmcOptimization.csv -sub-01/ses-01/dwi/sub-01_ses-01_space-T1w_desc-3dSHORE_cnr.nii.gz -sub-01/ses-01/dwi/sub-01_ses-01_space-T1w_desc-brain_mask.nii.gz -sub-01/ses-01/dwi/sub-01_ses-01_space-T1w_desc-preproc_dwi.b -sub-01/ses-01/dwi/sub-01_ses-01_space-T1w_desc-preproc_dwi.bval -sub-01/ses-01/dwi/sub-01_ses-01_space-T1w_desc-preproc_dwi.bvec -sub-01/ses-01/dwi/sub-01_ses-01_space-T1w_desc-preproc_dwi.nii.gz -sub-01/ses-01/dwi/sub-01_ses-01_space-T1w_desc-preproc_dwi.json -sub-01/ses-01/dwi/sub-01_ses-01_space-T1w_desc-preproc_dwi.b_table.txt -sub-01/ses-01/dwi/sub-01_ses-01_space-T1w_dwiref.nii.gz +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-3dSHORE_cnr.nii.gz +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-brain_mask.nii.gz +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.b +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.bval +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.bvec +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.nii.gz +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.json +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.b_table.txt +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/workflows/anatomical/volume.py b/qsiprep/workflows/anatomical/volume.py index ce3fc1c3..d60355f9 100644 --- a/qsiprep/workflows/anatomical/volume.py +++ b/qsiprep/workflows/anatomical/volume.py @@ -1215,7 +1215,7 @@ def init_anat_derivatives_wf(anatomical_template) -> Workflow: ds_t1_mni_inv_warp = pe.Node( DerivativesDataSink( base_directory=config.execution.output_dir, - to="T1w", + to="ACPC", mode="image", suffix="xfm", **{"from": anatomical_template}, @@ -1227,10 +1227,10 @@ def init_anat_derivatives_wf(anatomical_template) -> Workflow: ds_t1_template_acpc_transform = pe.Node( DerivativesDataSink( base_directory=config.execution.output_dir, - to="T1wACPC", + to="ACPC", mode="image", suffix="xfm", - **{"from": "T1wNative"}, + **{"from": "anat"}, ), name="ds_t1_template_acpc_transforms", run_without_submitting=True, @@ -1239,10 +1239,10 @@ def init_anat_derivatives_wf(anatomical_template) -> Workflow: ds_t1_template_acpc_inv_transform = pe.Node( DerivativesDataSink( base_directory=config.execution.output_dir, - to="T1wNative", + to="anat", mode="image", suffix="xfm", - **{"from": "T1wACPC"}, + **{"from": "ACPC"}, ), name="ds_t1_template_acpc_inv_transforms", run_without_submitting=True, @@ -1254,7 +1254,7 @@ def init_anat_derivatives_wf(anatomical_template) -> Workflow: to=anatomical_template, mode="image", suffix="xfm", - **{"from": "T1w"}, + **{"from": "ACPC"}, ), name="ds_t1_mni_warp", run_without_submitting=True, diff --git a/qsiprep/workflows/dwi/derivatives.py b/qsiprep/workflows/dwi/derivatives.py index 3c53f9fa..b42c1370 100644 --- a/qsiprep/workflows/dwi/derivatives.py +++ b/qsiprep/workflows/dwi/derivatives.py @@ -58,12 +58,12 @@ def init_dwi_derivatives_wf(source_file) -> Workflow: (inputnode, ds_optimization, [('hmc_optimization_data', 'in_file')]) ]) # fmt:skip - # 4D DWI in T1wACPC space + # 4D DWI in ACPC space ds_dwi_t1 = pe.Node( DerivativesDataSink( source_file=source_file, base_directory=output_dir, - space="T1w", + space="ACPC", desc="preproc", suffix="dwi", extension=".nii.gz", @@ -77,7 +77,7 @@ def init_dwi_derivatives_wf(source_file) -> Workflow: DerivativesDataSink( source_file=source_file, base_directory=output_dir, - space="T1w", + space="ACPC", suffix="dwi", extension=".bval", desc="preproc", @@ -90,7 +90,7 @@ def init_dwi_derivatives_wf(source_file) -> Workflow: DerivativesDataSink( source_file=source_file, base_directory=output_dir, - space="T1w", + space="ACPC", suffix="dwi", extension=".bvec", desc="preproc", @@ -103,7 +103,7 @@ def init_dwi_derivatives_wf(source_file) -> Workflow: DerivativesDataSink( source_file=source_file, base_directory=output_dir, - space="T1w", + space="ACPC", suffix="dwiref", extension=".nii.gz", compress=True, @@ -116,7 +116,7 @@ def init_dwi_derivatives_wf(source_file) -> Workflow: DerivativesDataSink( source_file=source_file, base_directory=output_dir, - space="T1w", + space="ACPC", desc="brain", suffix="mask", extension=".nii.gz", @@ -130,7 +130,7 @@ def init_dwi_derivatives_wf(source_file) -> Workflow: DerivativesDataSink( source_file=source_file, base_directory=output_dir, - space="T1w", + space="ACPC", desc=config.workflow.hmc_model, suffix="cnr", extension=".nii.gz", @@ -144,7 +144,7 @@ def init_dwi_derivatives_wf(source_file) -> Workflow: DerivativesDataSink( source_file=source_file, base_directory=output_dir, - space="T1w", + space="ACPC", desc="preproc", suffix="dwi", extension=".b", @@ -157,7 +157,7 @@ def init_dwi_derivatives_wf(source_file) -> Workflow: DerivativesDataSink( source_file=source_file, base_directory=output_dir, - space="T1w", + space="ACPC", desc="preproc", suffix="dwi", extension=".b_table.txt", @@ -183,7 +183,7 @@ def init_dwi_derivatives_wf(source_file) -> Workflow: # DerivativesDataSink( # base_directory=output_dir, # source_file=source_file, - # space="T1w", + # space="ACPC", # suffix="bvec", # compress=True, # ), diff --git a/qsiprep/workflows/dwi/finalize.py b/qsiprep/workflows/dwi/finalize.py index f7e0450e..0738a3a3 100644 --- a/qsiprep/workflows/dwi/finalize.py +++ b/qsiprep/workflows/dwi/finalize.py @@ -364,7 +364,7 @@ def init_dwi_finalize_wf( DerivativesDataSink( extension=".json", source_file=source_file, - space="T1w", + space="ACPC", desc="preproc", base_directory=config.execution.output_dir, ), From 2cdecd44b25b58546f7d053fd5357582734c373c Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 11 Nov 2024 09:41:18 -0500 Subject: [PATCH 02/12] Change orig transform name. --- qsiprep/workflows/anatomical/volume.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qsiprep/workflows/anatomical/volume.py b/qsiprep/workflows/anatomical/volume.py index d60355f9..91561bde 100644 --- a/qsiprep/workflows/anatomical/volume.py +++ b/qsiprep/workflows/anatomical/volume.py @@ -1202,7 +1202,7 @@ def init_anat_derivatives_wf(anatomical_template) -> Workflow: ds_t1_template_transforms = pe.MapNode( DerivativesDataSink( base_directory=config.execution.output_dir, - to="T1w", + to="anat", mode="image", suffix="xfm", **{"from": "orig"}, From 91002ef88b895c6c80119046ef22b888ab0c9fa3 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 11 Nov 2024 09:51:05 -0500 Subject: [PATCH 03/12] Add space-ACPC to ACPC-space anatomical outputs. --- .circleci/DSCSDSI_outputs.txt | 12 ++++++------ .circleci/DSDTI_nofmap_outputs.txt | 12 ++++++------ .circleci/DSDTI_outputs.txt | 12 ++++++------ .circleci/DSDTI_synsdc_outputs.txt | 12 ++++++------ .circleci/IntramodalTemplate_outputs.txt | 12 ++++++------ .circleci/get_data.sh | 12 ++++++------ qsiprep/tests/data/dscsdsi_outputs.txt | 10 +++++----- qsiprep/tests/data/dsdti_nofmap_outputs.txt | 10 +++++----- qsiprep/tests/data/dsdti_synfmap_outputs.txt | 10 +++++----- qsiprep/tests/data/dsdti_topup_outputs.txt | 10 +++++----- qsiprep/tests/data/forrest_gump_outputs.txt | 10 +++++----- qsiprep/tests/data/intramodal_template_outputs.txt | 12 ++++++------ .../tests/data/maternal_brain_project_outputs.txt | 10 +++++----- qsiprep/workflows/anatomical/volume.py | 1 + 14 files changed, 73 insertions(+), 72 deletions(-) diff --git a/.circleci/DSCSDSI_outputs.txt b/.circleci/DSCSDSI_outputs.txt index 51f67c70..104d860a 100644 --- a/.circleci/DSCSDSI_outputs.txt +++ b/.circleci/DSCSDSI_outputs.txt @@ -6,15 +6,15 @@ qsiprep/logs/CITATION.md qsiprep/logs/CITATION.tex qsiprep/sub-tester qsiprep/sub-tester/anat -qsiprep/sub-tester/anat/sub-tester_desc-brain_mask.nii.gz -qsiprep/sub-tester/anat/sub-tester_desc-preproc_T1w.nii.gz -qsiprep/sub-tester/anat/sub-tester_dseg.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_desc-brain_mask.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_desc-preproc_T1w.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_dseg.nii.gz qsiprep/sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 qsiprep/sub-tester/anat/sub-tester_from-orig_to-T1w_mode-image_xfm.txt qsiprep/sub-tester/anat/sub-tester_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -qsiprep/sub-tester/anat/sub-tester_label-CSF_probseg.nii.gz -qsiprep/sub-tester/anat/sub-tester_label-GM_probseg.nii.gz -qsiprep/sub-tester/anat/sub-tester_label-WM_probseg.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_label-CSF_probseg.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_label-GM_probseg.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_label-WM_probseg.nii.gz qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_dseg.nii.gz diff --git a/.circleci/DSDTI_nofmap_outputs.txt b/.circleci/DSDTI_nofmap_outputs.txt index 7c5eb983..2473beb3 100644 --- a/.circleci/DSDTI_nofmap_outputs.txt +++ b/.circleci/DSDTI_nofmap_outputs.txt @@ -6,15 +6,15 @@ qsiprep/logs/CITATION.md qsiprep/logs/CITATION.tex qsiprep/sub-PNC qsiprep/sub-PNC/anat -qsiprep/sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_dseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_desc-brain_mask.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz qsiprep/sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 qsiprep/sub-PNC/anat/sub-PNC_from-orig_to-T1w_mode-image_xfm.txt qsiprep/sub-PNC/anat/sub-PNC_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -qsiprep/sub-PNC/anat/sub-PNC_label-CSF_probseg.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_label-GM_probseg.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_label-WM_probseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-CSF_probseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-GM_probseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-WM_probseg.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_dseg.nii.gz diff --git a/.circleci/DSDTI_outputs.txt b/.circleci/DSDTI_outputs.txt index cad7326d..7e9cd047 100644 --- a/.circleci/DSDTI_outputs.txt +++ b/.circleci/DSDTI_outputs.txt @@ -6,15 +6,15 @@ qsiprep/logs/CITATION.md qsiprep/logs/CITATION.tex qsiprep/sub-PNC qsiprep/sub-PNC/anat -qsiprep/sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_dseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_desc-brain_mask.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz qsiprep/sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 qsiprep/sub-PNC/anat/sub-PNC_from-orig_to-T1w_mode-image_xfm.txt qsiprep/sub-PNC/anat/sub-PNC_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -qsiprep/sub-PNC/anat/sub-PNC_label-CSF_probseg.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_label-GM_probseg.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_label-WM_probseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-CSF_probseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-GM_probseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-WM_probseg.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_dseg.nii.gz diff --git a/.circleci/DSDTI_synsdc_outputs.txt b/.circleci/DSDTI_synsdc_outputs.txt index bac25180..94adcab3 100644 --- a/.circleci/DSDTI_synsdc_outputs.txt +++ b/.circleci/DSDTI_synsdc_outputs.txt @@ -6,15 +6,15 @@ qsiprep/logs/CITATION.md qsiprep/logs/CITATION.tex qsiprep/sub-PNC qsiprep/sub-PNC/anat -qsiprep/sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_dseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_desc-brain_mask.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz qsiprep/sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 qsiprep/sub-PNC/anat/sub-PNC_from-orig_to-T1w_mode-image_xfm.txt qsiprep/sub-PNC/anat/sub-PNC_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -qsiprep/sub-PNC/anat/sub-PNC_label-CSF_probseg.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_label-GM_probseg.nii.gz -qsiprep/sub-PNC/anat/sub-PNC_label-WM_probseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-CSF_probseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-GM_probseg.nii.gz +qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-WM_probseg.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_dseg.nii.gz diff --git a/.circleci/IntramodalTemplate_outputs.txt b/.circleci/IntramodalTemplate_outputs.txt index 85579125..5376fd9e 100644 --- a/.circleci/IntramodalTemplate_outputs.txt +++ b/.circleci/IntramodalTemplate_outputs.txt @@ -6,14 +6,14 @@ qsiprep/logs/CITATION.md qsiprep/logs/CITATION.tex qsiprep/sub-tester qsiprep/sub-tester/anat -qsiprep/sub-tester/anat/sub-tester_desc-brain_mask.nii.gz -qsiprep/sub-tester/anat/sub-tester_desc-preproc_T1w.nii.gz -qsiprep/sub-tester/anat/sub-tester_dseg.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_desc-brain_mask.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_desc-preproc_T1w.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_dseg.nii.gz qsiprep/sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 qsiprep/sub-tester/anat/sub-tester_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -qsiprep/sub-tester/anat/sub-tester_label-CSF_probseg.nii.gz -qsiprep/sub-tester/anat/sub-tester_label-GM_probseg.nii.gz -qsiprep/sub-tester/anat/sub-tester_label-WM_probseg.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_label-CSF_probseg.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_label-GM_probseg.nii.gz +qsiprep/sub-tester/anat/sub-tester_space-ACPC_label-WM_probseg.nii.gz qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_dseg.nii.gz diff --git a/.circleci/get_data.sh b/.circleci/get_data.sh index a66e1eb2..ed6a8689 100644 --- a/.circleci/get_data.sh +++ b/.circleci/get_data.sh @@ -312,15 +312,15 @@ Contents: - data/singleshell_output/qsiprep/logs/CITATION.html - data/singleshell_output/qsiprep/logs/CITATION.md - data/singleshell_output/qsiprep/logs/CITATION.tex - - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz - - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz - - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_dseg.nii.gz + - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_desc-brain_mask.nii.gz + - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz + - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_from-orig_to-T1w_mode-image_xfm.txt - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 - - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_label-CSF_probseg.nii.gz - - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_label-GM_probseg.nii.gz - - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_label-WM_probseg.nii.gz + - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-CSF_probseg.nii.gz + - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-GM_probseg.nii.gz + - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_space-ACPC_label-WM_probseg.nii.gz - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz - data/singleshell_output/qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_dseg.nii.gz diff --git a/qsiprep/tests/data/dscsdsi_outputs.txt b/qsiprep/tests/data/dscsdsi_outputs.txt index a8b135e9..f335fdfc 100644 --- a/qsiprep/tests/data/dscsdsi_outputs.txt +++ b/qsiprep/tests/data/dscsdsi_outputs.txt @@ -7,11 +7,11 @@ logs/CITATION.tex sub-tester sub-tester.html sub-tester/anat -sub-tester/anat/sub-tester_desc-aseg_dseg.nii.gz -sub-tester/anat/sub-tester_desc-brain_mask.nii.gz -sub-tester/anat/sub-tester_desc-preproc_T1w.json -sub-tester/anat/sub-tester_desc-preproc_T1w.nii.gz -sub-tester/anat/sub-tester_dseg.nii.gz +sub-tester/anat/sub-tester_space-ACPC_desc-aseg_dseg.nii.gz +sub-tester/anat/sub-tester_space-ACPC_desc-brain_mask.nii.gz +sub-tester/anat/sub-tester_space-ACPC_desc-preproc_T1w.json +sub-tester/anat/sub-tester_space-ACPC_desc-preproc_T1w.nii.gz +sub-tester/anat/sub-tester_space-ACPC_dseg.nii.gz sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 sub-tester/anat/sub-tester_from-ACPC_to-anat_mode-image_xfm.mat sub-tester/anat/sub-tester_from-anat_to-ACPC_mode-image_xfm.mat diff --git a/qsiprep/tests/data/dsdti_nofmap_outputs.txt b/qsiprep/tests/data/dsdti_nofmap_outputs.txt index d8c690d7..c84fc704 100644 --- a/qsiprep/tests/data/dsdti_nofmap_outputs.txt +++ b/qsiprep/tests/data/dsdti_nofmap_outputs.txt @@ -7,11 +7,11 @@ logs/CITATION.tex sub-PNC sub-PNC.html sub-PNC/anat -sub-PNC/anat/sub-PNC_desc-aseg_dseg.nii.gz -sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz -sub-PNC/anat/sub-PNC_desc-preproc_T1w.json -sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz -sub-PNC/anat/sub-PNC_dseg.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_desc-aseg_dseg.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_desc-brain_mask.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.json +sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat diff --git a/qsiprep/tests/data/dsdti_synfmap_outputs.txt b/qsiprep/tests/data/dsdti_synfmap_outputs.txt index d8c690d7..c84fc704 100644 --- a/qsiprep/tests/data/dsdti_synfmap_outputs.txt +++ b/qsiprep/tests/data/dsdti_synfmap_outputs.txt @@ -7,11 +7,11 @@ logs/CITATION.tex sub-PNC sub-PNC.html sub-PNC/anat -sub-PNC/anat/sub-PNC_desc-aseg_dseg.nii.gz -sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz -sub-PNC/anat/sub-PNC_desc-preproc_T1w.json -sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz -sub-PNC/anat/sub-PNC_dseg.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_desc-aseg_dseg.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_desc-brain_mask.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.json +sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat diff --git a/qsiprep/tests/data/dsdti_topup_outputs.txt b/qsiprep/tests/data/dsdti_topup_outputs.txt index d8c690d7..c84fc704 100644 --- a/qsiprep/tests/data/dsdti_topup_outputs.txt +++ b/qsiprep/tests/data/dsdti_topup_outputs.txt @@ -7,11 +7,11 @@ logs/CITATION.tex sub-PNC sub-PNC.html sub-PNC/anat -sub-PNC/anat/sub-PNC_desc-aseg_dseg.nii.gz -sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz -sub-PNC/anat/sub-PNC_desc-preproc_T1w.json -sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz -sub-PNC/anat/sub-PNC_dseg.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_desc-aseg_dseg.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_desc-brain_mask.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.json +sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz +sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat diff --git a/qsiprep/tests/data/forrest_gump_outputs.txt b/qsiprep/tests/data/forrest_gump_outputs.txt index 9733a1b5..7857cc96 100644 --- a/qsiprep/tests/data/forrest_gump_outputs.txt +++ b/qsiprep/tests/data/forrest_gump_outputs.txt @@ -7,11 +7,11 @@ logs/CITATION.tex sub-01 sub-01.html sub-01/anat -sub-01/anat/sub-01_desc-aseg_dseg.nii.gz -sub-01/anat/sub-01_desc-brain_mask.nii.gz -sub-01/anat/sub-01_desc-preproc_T1w.json -sub-01/anat/sub-01_desc-preproc_T1w.nii.gz -sub-01/anat/sub-01_dseg.nii.gz +sub-01/anat/sub-01_space-ACPC_desc-aseg_dseg.nii.gz +sub-01/anat/sub-01_space-ACPC_desc-brain_mask.nii.gz +sub-01/anat/sub-01_space-ACPC_desc-preproc_T1w.json +sub-01/anat/sub-01_space-ACPC_desc-preproc_T1w.nii.gz +sub-01/anat/sub-01_space-ACPC_dseg.nii.gz sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 sub-01/anat/sub-01_from-ACPC_to-anat_mode-image_xfm.mat sub-01/anat/sub-01_from-anat_to-ACPC_mode-image_xfm.mat diff --git a/qsiprep/tests/data/intramodal_template_outputs.txt b/qsiprep/tests/data/intramodal_template_outputs.txt index f2a2bc8d..4bce17b5 100644 --- a/qsiprep/tests/data/intramodal_template_outputs.txt +++ b/qsiprep/tests/data/intramodal_template_outputs.txt @@ -7,14 +7,14 @@ logs/CITATION.tex sub-tester sub-tester.html sub-tester/anat -sub-tester/anat/sub-tester_desc-brain_mask.nii.gz -sub-tester/anat/sub-tester_desc-preproc_T1w.nii.gz -sub-tester/anat/sub-tester_dseg.nii.gz +sub-tester/anat/sub-tester_space-ACPC_desc-brain_mask.nii.gz +sub-tester/anat/sub-tester_space-ACPC_desc-preproc_T1w.nii.gz +sub-tester/anat/sub-tester_space-ACPC_dseg.nii.gz sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 sub-tester/anat/sub-tester_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -sub-tester/anat/sub-tester_label-CSF_probseg.nii.gz -sub-tester/anat/sub-tester_label-GM_probseg.nii.gz -sub-tester/anat/sub-tester_label-WM_probseg.nii.gz +sub-tester/anat/sub-tester_space-ACPC_label-CSF_probseg.nii.gz +sub-tester/anat/sub-tester_space-ACPC_label-GM_probseg.nii.gz +sub-tester/anat/sub-tester_space-ACPC_label-WM_probseg.nii.gz sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_dseg.nii.gz diff --git a/qsiprep/tests/data/maternal_brain_project_outputs.txt b/qsiprep/tests/data/maternal_brain_project_outputs.txt index 3878e4e0..947719df 100644 --- a/qsiprep/tests/data/maternal_brain_project_outputs.txt +++ b/qsiprep/tests/data/maternal_brain_project_outputs.txt @@ -7,11 +7,11 @@ logs/CITATION.tex sub-01 sub-01.html sub-01/anat -sub-01/anat/sub-01_desc-aseg_dseg.nii.gz -sub-01/anat/sub-01_desc-brain_mask.nii.gz -sub-01/anat/sub-01_desc-preproc_T1w.json -sub-01/anat/sub-01_desc-preproc_T1w.nii.gz -sub-01/anat/sub-01_dseg.nii.gz +sub-01/anat/sub-01_space-ACPC_desc-aseg_dseg.nii.gz +sub-01/anat/sub-01_space-ACPC_desc-brain_mask.nii.gz +sub-01/anat/sub-01_space-ACPC_desc-preproc_T1w.json +sub-01/anat/sub-01_space-ACPC_desc-preproc_T1w.nii.gz +sub-01/anat/sub-01_space-ACPC_dseg.nii.gz sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 sub-01/anat/sub-01_from-ACPC_to-anat_mode-image_xfm.mat sub-01/anat/sub-01_from-anat_to-ACPC_mode-image_xfm.mat diff --git a/qsiprep/workflows/anatomical/volume.py b/qsiprep/workflows/anatomical/volume.py index 91561bde..ef736cb4 100644 --- a/qsiprep/workflows/anatomical/volume.py +++ b/qsiprep/workflows/anatomical/volume.py @@ -1159,6 +1159,7 @@ def init_anat_derivatives_wf(anatomical_template) -> Workflow: DerivativesDataSink( compress=True, base_directory=config.execution.output_dir, + space="ACPC", desc="preproc", keep_dtype=True, ), From 15b449f3d11f76f55b84bdcfa951ad835263e063 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 11 Nov 2024 09:51:57 -0500 Subject: [PATCH 04/12] Add ACPC to DDSes. --- qsiprep/workflows/anatomical/volume.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/qsiprep/workflows/anatomical/volume.py b/qsiprep/workflows/anatomical/volume.py index ef736cb4..242dc1e1 100644 --- a/qsiprep/workflows/anatomical/volume.py +++ b/qsiprep/workflows/anatomical/volume.py @@ -1171,6 +1171,7 @@ def init_anat_derivatives_wf(anatomical_template) -> Workflow: DerivativesDataSink( compress=True, base_directory=config.execution.output_dir, + space="ACPC", desc="brain", suffix="mask", ), @@ -1182,6 +1183,7 @@ def init_anat_derivatives_wf(anatomical_template) -> Workflow: DerivativesDataSink( compress=True, base_directory=config.execution.output_dir, + space="ACPC", suffix="dseg", ), name="ds_t1_seg", @@ -1192,6 +1194,7 @@ def init_anat_derivatives_wf(anatomical_template) -> Workflow: DerivativesDataSink( compress=True, base_directory=config.execution.output_dir, + space="ACPC", desc="aseg", suffix="dseg", ), From dcc15190977a3212c65a0148ebbb03bd6fbde849 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 11 Nov 2024 10:48:54 -0500 Subject: [PATCH 05/12] Reorder expected outputs. --- qsiprep/tests/data/drbuddi_rpe_outputs.txt | 4 ++-- .../tests/data/drbuddi_shoreline_epi_outputs.txt | 4 ++-- .../tests/data/drbuddi_tensorline_epi_outputs.txt | 4 ++-- qsiprep/tests/data/dscsdsi_outputs.txt | 14 +++++++------- qsiprep/tests/data/dsdti_nofmap_outputs.txt | 14 +++++++------- qsiprep/tests/data/dsdti_synfmap_outputs.txt | 14 +++++++------- qsiprep/tests/data/dsdti_topup_outputs.txt | 14 +++++++------- qsiprep/tests/data/forrest_gump_outputs.txt | 12 ++++++------ qsiprep/tests/data/intramodal_template_outputs.txt | 8 ++++---- .../tests/data/maternal_brain_project_outputs.txt | 12 ++++++------ 10 files changed, 50 insertions(+), 50 deletions(-) diff --git a/qsiprep/tests/data/drbuddi_rpe_outputs.txt b/qsiprep/tests/data/drbuddi_rpe_outputs.txt index ce6749bc..6bd70d99 100644 --- a/qsiprep/tests/data/drbuddi_rpe_outputs.txt +++ b/qsiprep/tests/data/drbuddi_rpe_outputs.txt @@ -13,9 +13,9 @@ sub-tinytensors/dwi/sub-tinytensors_desc-SliceQC_dwi.json sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-brain_mask.nii.gz sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-eddy_cnr.nii.gz sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.b +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.b_table.txt sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.bval sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.bvec -sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.nii.gz sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.json -sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.b_table.txt +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.nii.gz sub-tinytensors/dwi/sub-tinytensors_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt b/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt index 3e728570..b1cc3cf2 100644 --- a/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt +++ b/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt @@ -13,9 +13,9 @@ sub-tinytensors/dwi/sub-tinytensors_dir-PA_desc-SliceQC_dwi.json sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-brain_mask.nii.gz sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-none_cnr.nii.gz sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.b +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.b_table.txt sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.bval sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.bvec -sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.nii.gz sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.json -sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.b_table.txt +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.nii.gz sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt b/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt index 1bb1cb0e..6d16d614 100644 --- a/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt +++ b/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt @@ -12,10 +12,10 @@ sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec -sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-tensor_cnr.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/dscsdsi_outputs.txt b/qsiprep/tests/data/dscsdsi_outputs.txt index f335fdfc..0fdb08a1 100644 --- a/qsiprep/tests/data/dscsdsi_outputs.txt +++ b/qsiprep/tests/data/dscsdsi_outputs.txt @@ -7,16 +7,16 @@ logs/CITATION.tex sub-tester sub-tester.html sub-tester/anat +sub-tester/anat/sub-tester_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-tester/anat/sub-tester_from-ACPC_to-anat_mode-image_xfm.mat +sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-tester/anat/sub-tester_from-anat_to-ACPC_mode-image_xfm.mat +sub-tester/anat/sub-tester_from-orig_to-anat_mode-image_xfm.txt sub-tester/anat/sub-tester_space-ACPC_desc-aseg_dseg.nii.gz sub-tester/anat/sub-tester_space-ACPC_desc-brain_mask.nii.gz sub-tester/anat/sub-tester_space-ACPC_desc-preproc_T1w.json sub-tester/anat/sub-tester_space-ACPC_desc-preproc_T1w.nii.gz sub-tester/anat/sub-tester_space-ACPC_dseg.nii.gz -sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 -sub-tester/anat/sub-tester_from-ACPC_to-anat_mode-image_xfm.mat -sub-tester/anat/sub-tester_from-anat_to-ACPC_mode-image_xfm.mat -sub-tester/anat/sub-tester_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -sub-tester/anat/sub-tester_from-orig_to-anat_mode-image_xfm.txt sub-tester/dwi sub-tester/dwi/sub-tester_acq-HASC55AP_confounds.tsv sub-tester/dwi/sub-tester_acq-HASC55AP_desc-ImageQC_dwi.csv @@ -24,9 +24,9 @@ sub-tester/dwi/sub-tester_acq-HASC55AP_desc-SliceQC_dwi.json sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-3dSHORE_cnr.nii.gz sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-brain_mask.nii.gz sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b_table.txt sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bval sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bvec -sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.nii.gz sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.json -sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b_table.txt +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.nii.gz sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/dsdti_nofmap_outputs.txt b/qsiprep/tests/data/dsdti_nofmap_outputs.txt index c84fc704..7f0c1f26 100644 --- a/qsiprep/tests/data/dsdti_nofmap_outputs.txt +++ b/qsiprep/tests/data/dsdti_nofmap_outputs.txt @@ -7,16 +7,16 @@ logs/CITATION.tex sub-PNC sub-PNC.html sub-PNC/anat +sub-PNC/anat/sub-PNC_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-orig_to-anat_mode-image_xfm.txt sub-PNC/anat/sub-PNC_space-ACPC_desc-aseg_dseg.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_desc-brain_mask.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.json sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz -sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-orig_to-anat_mode-image_xfm.txt sub-PNC/dwi sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv @@ -24,9 +24,9 @@ sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec -sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/dsdti_synfmap_outputs.txt b/qsiprep/tests/data/dsdti_synfmap_outputs.txt index c84fc704..7f0c1f26 100644 --- a/qsiprep/tests/data/dsdti_synfmap_outputs.txt +++ b/qsiprep/tests/data/dsdti_synfmap_outputs.txt @@ -7,16 +7,16 @@ logs/CITATION.tex sub-PNC sub-PNC.html sub-PNC/anat +sub-PNC/anat/sub-PNC_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-orig_to-anat_mode-image_xfm.txt sub-PNC/anat/sub-PNC_space-ACPC_desc-aseg_dseg.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_desc-brain_mask.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.json sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz -sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-orig_to-anat_mode-image_xfm.txt sub-PNC/dwi sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv @@ -24,9 +24,9 @@ sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec -sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/dsdti_topup_outputs.txt b/qsiprep/tests/data/dsdti_topup_outputs.txt index c84fc704..7f0c1f26 100644 --- a/qsiprep/tests/data/dsdti_topup_outputs.txt +++ b/qsiprep/tests/data/dsdti_topup_outputs.txt @@ -7,16 +7,16 @@ logs/CITATION.tex sub-PNC sub-PNC.html sub-PNC/anat +sub-PNC/anat/sub-PNC_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat +sub-PNC/anat/sub-PNC_from-orig_to-anat_mode-image_xfm.txt sub-PNC/anat/sub-PNC_space-ACPC_desc-aseg_dseg.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_desc-brain_mask.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.json sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz -sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-ACPC_to-anat_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-anat_to-ACPC_mode-image_xfm.mat -sub-PNC/anat/sub-PNC_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -sub-PNC/anat/sub-PNC_from-orig_to-anat_mode-image_xfm.txt sub-PNC/dwi sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv @@ -24,9 +24,9 @@ sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec -sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json -sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/forrest_gump_outputs.txt b/qsiprep/tests/data/forrest_gump_outputs.txt index 7857cc96..825fb1d9 100644 --- a/qsiprep/tests/data/forrest_gump_outputs.txt +++ b/qsiprep/tests/data/forrest_gump_outputs.txt @@ -7,15 +7,15 @@ logs/CITATION.tex sub-01 sub-01.html sub-01/anat +sub-01/anat/sub-01_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-01/anat/sub-01_from-ACPC_to-anat_mode-image_xfm.mat +sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-01/anat/sub-01_from-anat_to-ACPC_mode-image_xfm.mat sub-01/anat/sub-01_space-ACPC_desc-aseg_dseg.nii.gz sub-01/anat/sub-01_space-ACPC_desc-brain_mask.nii.gz sub-01/anat/sub-01_space-ACPC_desc-preproc_T1w.json sub-01/anat/sub-01_space-ACPC_desc-preproc_T1w.nii.gz sub-01/anat/sub-01_space-ACPC_dseg.nii.gz -sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 -sub-01/anat/sub-01_from-ACPC_to-anat_mode-image_xfm.mat -sub-01/anat/sub-01_from-anat_to-ACPC_mode-image_xfm.mat -sub-01/anat/sub-01_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 sub-01/ses-forrestgump sub-01/ses-forrestgump/anat sub-01/ses-forrestgump/anat/sub-01_ses-forrestgump_rec-autobox_from-orig_to-anat_mode-image_xfm.txt @@ -26,9 +26,9 @@ sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_desc-SliceQC_dwi.json sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-brain_mask.nii.gz sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-eddy_cnr.nii.gz sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.b +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.b_table.txt sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.bval sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.bvec -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.nii.gz sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.json -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.b_table.txt +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.nii.gz sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/intramodal_template_outputs.txt b/qsiprep/tests/data/intramodal_template_outputs.txt index 4bce17b5..a0d6ffce 100644 --- a/qsiprep/tests/data/intramodal_template_outputs.txt +++ b/qsiprep/tests/data/intramodal_template_outputs.txt @@ -7,11 +7,11 @@ logs/CITATION.tex sub-tester sub-tester.html sub-tester/anat +sub-tester/anat/sub-tester_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 sub-tester/anat/sub-tester_space-ACPC_desc-brain_mask.nii.gz sub-tester/anat/sub-tester_space-ACPC_desc-preproc_T1w.nii.gz sub-tester/anat/sub-tester_space-ACPC_dseg.nii.gz -sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 -sub-tester/anat/sub-tester_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 sub-tester/anat/sub-tester_space-ACPC_label-CSF_probseg.nii.gz sub-tester/anat/sub-tester_space-ACPC_label-GM_probseg.nii.gz sub-tester/anat/sub-tester_space-ACPC_label-WM_probseg.nii.gz @@ -49,8 +49,8 @@ sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-none_cnr.nii. sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.b sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.bval sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.bvec -sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.nii.gz sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.json +sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.nii.gz sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_dwiref.nii.gz sub-tester/ses-2 sub-tester/ses-2/dwi @@ -62,6 +62,6 @@ sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-none_cnr.nii. sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bval sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bvec -sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.nii.gz sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.json +sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.nii.gz sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_dwiref.nii.gz diff --git a/qsiprep/tests/data/maternal_brain_project_outputs.txt b/qsiprep/tests/data/maternal_brain_project_outputs.txt index 947719df..98389ff6 100644 --- a/qsiprep/tests/data/maternal_brain_project_outputs.txt +++ b/qsiprep/tests/data/maternal_brain_project_outputs.txt @@ -7,15 +7,15 @@ logs/CITATION.tex sub-01 sub-01.html sub-01/anat +sub-01/anat/sub-01_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 +sub-01/anat/sub-01_from-ACPC_to-anat_mode-image_xfm.mat +sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 +sub-01/anat/sub-01_from-anat_to-ACPC_mode-image_xfm.mat sub-01/anat/sub-01_space-ACPC_desc-aseg_dseg.nii.gz sub-01/anat/sub-01_space-ACPC_desc-brain_mask.nii.gz sub-01/anat/sub-01_space-ACPC_desc-preproc_T1w.json sub-01/anat/sub-01_space-ACPC_desc-preproc_T1w.nii.gz sub-01/anat/sub-01_space-ACPC_dseg.nii.gz -sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 -sub-01/anat/sub-01_from-ACPC_to-anat_mode-image_xfm.mat -sub-01/anat/sub-01_from-anat_to-ACPC_mode-image_xfm.mat -sub-01/anat/sub-01_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 sub-01/ses-01 sub-01/ses-01/anat sub-01/ses-01/anat/sub-01_ses-01_rec-autobox_from-orig_to-anat_mode-image_xfm.txt @@ -27,9 +27,9 @@ sub-01/ses-01/dwi/sub-01_ses-01_hmcOptimization.csv sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-3dSHORE_cnr.nii.gz sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-brain_mask.nii.gz sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.b +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.b_table.txt sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.bval sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.bvec -sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.nii.gz sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.json -sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.b_table.txt +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.nii.gz sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_dwiref.nii.gz From d4286d5ece4041aae1f3751f862dfdea8c4bc2d9 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 11 Nov 2024 11:00:03 -0500 Subject: [PATCH 06/12] Update output documentation. --- docs/preprocessing.rst | 69 ++++++++++++++++++++---------------------- 1 file changed, 32 insertions(+), 37 deletions(-) diff --git a/docs/preprocessing.rst b/docs/preprocessing.rst index 42269c67..844f8907 100644 --- a/docs/preprocessing.rst +++ b/docs/preprocessing.rst @@ -167,9 +167,6 @@ they are concatenated. When warped groups are concatenated an additional b=0 image intensity normalization is performed. - - - Preprocessing HCP-style ^^^^^^^^^^^^^^^^^^^^^^^ @@ -214,11 +211,10 @@ qsiprep generates three broad classes of outcomes: Visual Reports ^^^^^^^^^^^^^^^ -qsiprep outputs summary reports, written to ``/qsiprep/sub-.html``. These reports provide a quick way to -make visual inspection of the results easy. One useful graphic is the -animation of the q-space sampling scheme before and after the pipeline. Here -is a sampling scheme from a DSI scan: +qsiprep outputs summary reports, written to ``/qsiprep/sub-.html``. +These reports provide a quick way to make visual inspection of the results easy. +One useful graphic is the animation of the q-space sampling scheme before and after the pipeline. +Here is a sampling scheme from a DSI scan: .. figure:: _static/sampling_scheme.gif :scale: 75% @@ -231,35 +227,34 @@ is a sampling scheme from a DSI scan: Preprocessed data (qsiprep *derivatives*) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -There are additional files, called "Derivatives", written to -``/qsiprep/sub-/``. - -Derivatives related to T1w files are nearly identical to those produced by ``FMRIPREP`` and -can be found in the ``anat`` subfolder: - -- ``*T1w_brainmask.nii.gz`` Brain mask derived using ANTs' ``antsBrainExtraction.sh``. -- ``*T1w_class-CSF_probtissue.nii.gz`` -- ``*T1w_class-GM_probtissue.nii.gz`` -- ``*T1w_class-WM_probtissue.nii.gz`` tissue-probability maps. -- ``*T1w_dtissue.nii.gz`` Tissue class map derived using FAST. -- ``*T1w_preproc.nii.gz`` Bias field corrected T1w file, using ANTS' N4BiasFieldCorrection -- ``*T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz`` Same as ``_brainmask`` above, but in MNI space. -- ``*T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz`` -- ``*T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz`` -- ``*T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz`` Probability tissue maps, transformed into MNI space -- ``*T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz`` Same as ``_dtissue`` above, but in MNI space -- ``*T1w_space-MNI152NLin2009cAsym_preproc.nii.gz`` Same as ``_preproc`` above, but in MNI space -- ``*T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5`` Composite (warp and affine) transform to map from MNI to T1 space -- ``*T1w_target-MNI152NLin2009cAsym_warp.h5`` Composite (warp and affine) transform to transform T1w into MNI space - -.. Note: - These are in LPS+ orientation, so are not identical to FMRIPREP's anatomical outputs +There are additional files, called "Derivatives", +written to ``/qsiprep/sub-/``. + +Derivatives related to anatomical files are nearly identical to those produced by ``fMRIprep`` and +can be found in the ``anat`` subfolder. +One major difference is that the anatomical derivatives are in LPS+ orientation and are realigned to the AC-PC, +while ``fMRIprep``'s are in RAS+ orientation and retain the original anatomical images' orientation. + +- ``_space-ACPC_desc-brain_mask.nii.gz`` Brain mask derived using ANTs' ``antsBrainExtraction.sh``. +- ``_space-ACPC_label-CSF_probseg.nii.gz`` +- ``_space-ACPC_label-GM_probseg.nii.gz`` +- ``_space-ACPC_label-WM_probseg.nii.gz`` tissue-probability maps. +- ``_space-ACPC_dseg.nii.gz`` Tissue class map derived using FAST. +- ``_space-ACPC_desc-preproc_T1w.nii.gz`` Bias field corrected T1w file, using ANTS' N4BiasFieldCorrection +- ``_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz`` Same as ``_brainmask`` above, but in MNI space. +- ``_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz`` +- ``_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz`` +- ``_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz`` Probability tissue maps, transformed into MNI space +- ``_space-MNI152NLin2009cAsym_dseg.nii.gz`` Same as ``_dtissue`` above, but in MNI space +- ``_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz`` Same as ``_preproc`` above, but in MNI space +- ``_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5`` Composite (warp and affine) transform to map from MNI to ACPC space +- ``_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5`` Composite (warp and affine) transform to transform ACPC into MNI space Derivatives related to diffusion images are in the ``dwi`` subfolder. - ``*_confounds.tsv`` A tab-separated value file with one column per calculated confound and one row per timepoint/volume -Volumetric output spaces include ``T1w`` (default) and ``MNI152NLin2009cAsym``. +Volumetric outputs are written out in ``ACPC`` space. - ``*dwiref.nii.gz`` The b0 template - ``*desc-brain_mask.nii.gz`` The generous brain mask that should be reduced probably @@ -479,8 +474,8 @@ to be run through ``qsiprep``. Animation showing T1w to MNI normalization -Longitudinal T1w processing -~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Longitudinal anatomical processing +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In the case of multiple T1w images (across sessions and/or within a session), T1w images are merged into a single template image using FreeSurfer's @@ -495,11 +490,11 @@ flag, which forces the estimation of an unbiased template. .. note:: - The preprocessed T1w image defines the ``T1w`` space. + The preprocessed T1w image defines the ``anat`` space. In the case of multiple T1w images, this space may not be precisely aligned with any of the original images. Reconstructed surfaces and functional datasets will be registered to the - ``T1w`` space, and not to the input images. + ``anat`` space, and not to the input images. Processing Infant Data @@ -842,7 +837,7 @@ pipeline for DWIs .. _resampling: Pre-processed DWIs in a different space -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :func:`qsiprep.workflows.dwi.resampling.init_dwi_trans_wf` From 42d7c0489e1e1f7d879ad1bb8a1936569353ba26 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Tue, 12 Nov 2024 09:16:26 -0500 Subject: [PATCH 07/12] Add space-ACPC to QC files. --- .circleci/DSCSDSI_outputs.txt | 4 ++-- .circleci/DSDTI_nofmap_outputs.txt | 4 ++-- .circleci/DSDTI_outputs.txt | 4 ++-- .circleci/DSDTI_synsdc_outputs.txt | 4 ++-- .circleci/IntramodalTemplate_outputs.txt | 8 ++++---- qsiprep/tests/data/drbuddi_rpe_outputs.txt | 4 ++-- qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt | 4 ++-- qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt | 4 ++-- qsiprep/tests/data/dscsdsi_outputs.txt | 4 ++-- qsiprep/tests/data/dsdti_nofmap_outputs.txt | 4 ++-- qsiprep/tests/data/dsdti_synfmap_outputs.txt | 4 ++-- qsiprep/tests/data/dsdti_topup_outputs.txt | 4 ++-- qsiprep/tests/data/forrest_gump_outputs.txt | 4 ++-- qsiprep/tests/data/intramodal_template_outputs.txt | 8 ++++---- qsiprep/tests/data/maternal_brain_project_outputs.txt | 4 ++-- qsiprep/workflows/dwi/finalize.py | 6 ++++-- 16 files changed, 38 insertions(+), 36 deletions(-) diff --git a/.circleci/DSCSDSI_outputs.txt b/.circleci/DSCSDSI_outputs.txt index 104d860a..e47338be 100644 --- a/.circleci/DSCSDSI_outputs.txt +++ b/.circleci/DSCSDSI_outputs.txt @@ -23,8 +23,8 @@ qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-GM_probseg.ni qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz qsiprep/sub-tester/dwi qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_confounds.tsv -qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_desc-ImageQC_dwi.csv -qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_desc-SliceQC_dwi.json +qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-ImageQC_dwi.csv +qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-SliceQC_dwi.json qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_dwiqc.json qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-3dSHORE_cnr.nii.gz qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-brain_mask.nii.gz diff --git a/.circleci/DSDTI_nofmap_outputs.txt b/.circleci/DSDTI_nofmap_outputs.txt index 2473beb3..8e0c1263 100644 --- a/.circleci/DSDTI_nofmap_outputs.txt +++ b/.circleci/DSDTI_nofmap_outputs.txt @@ -23,8 +23,8 @@ qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz qsiprep/sub-PNC/dwi qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-ImageQC_dwi.csv +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-SliceQC_dwi.json qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_dwiqc.json qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz diff --git a/.circleci/DSDTI_outputs.txt b/.circleci/DSDTI_outputs.txt index 7e9cd047..8befe6c3 100644 --- a/.circleci/DSDTI_outputs.txt +++ b/.circleci/DSDTI_outputs.txt @@ -23,8 +23,8 @@ qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz qsiprep/sub-PNC/dwi qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-ImageQC_dwi.csv +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-SliceQC_dwi.json qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_dwiqc.json qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz diff --git a/.circleci/DSDTI_synsdc_outputs.txt b/.circleci/DSDTI_synsdc_outputs.txt index 94adcab3..fb334f96 100644 --- a/.circleci/DSDTI_synsdc_outputs.txt +++ b/.circleci/DSDTI_synsdc_outputs.txt @@ -23,8 +23,8 @@ qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz qsiprep/sub-PNC/dwi qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv -qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-ImageQC_dwi.csv +qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-SliceQC_dwi.json qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_dwiqc.json qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz diff --git a/.circleci/IntramodalTemplate_outputs.txt b/.circleci/IntramodalTemplate_outputs.txt index 5376fd9e..f4146e5e 100644 --- a/.circleci/IntramodalTemplate_outputs.txt +++ b/.circleci/IntramodalTemplate_outputs.txt @@ -42,8 +42,8 @@ qsiprep/sub-tester/ses-1/anat qsiprep/sub-tester/ses-1/anat/sub-tester_ses-1_from-orig_to-T1w_mode-image_xfm.txt qsiprep/sub-tester/ses-1/dwi qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_confounds.tsv -qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_desc-ImageQC_dwi.csv -qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_desc-SliceQC_dwi.json +qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-ImageQC_dwi.csv +qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-SliceQC_dwi.json qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_dwiqc.json qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-brain_mask.nii.gz qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-none_cnr.nii.gz @@ -55,8 +55,8 @@ qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_dwiref.nii qsiprep/sub-tester/ses-2 qsiprep/sub-tester/ses-2/dwi qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_confounds.tsv -qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_desc-ImageQC_dwi.csv -qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_desc-SliceQC_dwi.json +qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-ImageQC_dwi.csv +qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-SliceQC_dwi.json qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_dwiqc.json qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-brain_mask.nii.gz qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-none_cnr.nii.gz diff --git a/qsiprep/tests/data/drbuddi_rpe_outputs.txt b/qsiprep/tests/data/drbuddi_rpe_outputs.txt index 6bd70d99..9635d7a2 100644 --- a/qsiprep/tests/data/drbuddi_rpe_outputs.txt +++ b/qsiprep/tests/data/drbuddi_rpe_outputs.txt @@ -8,8 +8,8 @@ sub-tinytensors sub-tinytensors.html sub-tinytensors/dwi sub-tinytensors/dwi/sub-tinytensors_confounds.tsv -sub-tinytensors/dwi/sub-tinytensors_desc-ImageQC_dwi.csv -sub-tinytensors/dwi/sub-tinytensors_desc-SliceQC_dwi.json +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-ImageQC_dwi.csv +sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-SliceQC_dwi.json sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-brain_mask.nii.gz sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-eddy_cnr.nii.gz sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.b diff --git a/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt b/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt index b1cc3cf2..6fcd9f19 100644 --- a/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt +++ b/qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt @@ -8,8 +8,8 @@ sub-tinytensors sub-tinytensors.html sub-tinytensors/dwi sub-tinytensors/dwi/sub-tinytensors_dir-PA_confounds.tsv -sub-tinytensors/dwi/sub-tinytensors_dir-PA_desc-ImageQC_dwi.csv -sub-tinytensors/dwi/sub-tinytensors_dir-PA_desc-SliceQC_dwi.json +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-ImageQC_dwi.csv +sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-SliceQC_dwi.json sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-brain_mask.nii.gz sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-none_cnr.nii.gz sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.b diff --git a/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt b/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt index 6d16d614..29b317f2 100644 --- a/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt +++ b/qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt @@ -8,8 +8,8 @@ sub-PNC sub-PNC.html sub-PNC/dwi sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv -sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv -sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-ImageQC_dwi.csv +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-SliceQC_dwi.json sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt diff --git a/qsiprep/tests/data/dscsdsi_outputs.txt b/qsiprep/tests/data/dscsdsi_outputs.txt index 0fdb08a1..8eab6c12 100644 --- a/qsiprep/tests/data/dscsdsi_outputs.txt +++ b/qsiprep/tests/data/dscsdsi_outputs.txt @@ -19,9 +19,9 @@ sub-tester/anat/sub-tester_space-ACPC_desc-preproc_T1w.nii.gz sub-tester/anat/sub-tester_space-ACPC_dseg.nii.gz sub-tester/dwi sub-tester/dwi/sub-tester_acq-HASC55AP_confounds.tsv -sub-tester/dwi/sub-tester_acq-HASC55AP_desc-ImageQC_dwi.csv -sub-tester/dwi/sub-tester_acq-HASC55AP_desc-SliceQC_dwi.json sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-3dSHORE_cnr.nii.gz +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-ImageQC_dwi.csv +sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-SliceQC_dwi.json sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-brain_mask.nii.gz sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b_table.txt diff --git a/qsiprep/tests/data/dsdti_nofmap_outputs.txt b/qsiprep/tests/data/dsdti_nofmap_outputs.txt index 7f0c1f26..262e955d 100644 --- a/qsiprep/tests/data/dsdti_nofmap_outputs.txt +++ b/qsiprep/tests/data/dsdti_nofmap_outputs.txt @@ -19,8 +19,8 @@ sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz sub-PNC/dwi sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv -sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv -sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-ImageQC_dwi.csv +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-SliceQC_dwi.json sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b diff --git a/qsiprep/tests/data/dsdti_synfmap_outputs.txt b/qsiprep/tests/data/dsdti_synfmap_outputs.txt index 7f0c1f26..262e955d 100644 --- a/qsiprep/tests/data/dsdti_synfmap_outputs.txt +++ b/qsiprep/tests/data/dsdti_synfmap_outputs.txt @@ -19,8 +19,8 @@ sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz sub-PNC/dwi sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv -sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv -sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-ImageQC_dwi.csv +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-SliceQC_dwi.json sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b diff --git a/qsiprep/tests/data/dsdti_topup_outputs.txt b/qsiprep/tests/data/dsdti_topup_outputs.txt index 7f0c1f26..262e955d 100644 --- a/qsiprep/tests/data/dsdti_topup_outputs.txt +++ b/qsiprep/tests/data/dsdti_topup_outputs.txt @@ -19,8 +19,8 @@ sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz sub-PNC/dwi sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv -sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv -sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-ImageQC_dwi.csv +sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-SliceQC_dwi.json sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-eddy_cnr.nii.gz sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b diff --git a/qsiprep/tests/data/forrest_gump_outputs.txt b/qsiprep/tests/data/forrest_gump_outputs.txt index 825fb1d9..9ac5b51b 100644 --- a/qsiprep/tests/data/forrest_gump_outputs.txt +++ b/qsiprep/tests/data/forrest_gump_outputs.txt @@ -21,8 +21,8 @@ sub-01/ses-forrestgump/anat sub-01/ses-forrestgump/anat/sub-01_ses-forrestgump_rec-autobox_from-orig_to-anat_mode-image_xfm.txt sub-01/ses-forrestgump/dwi sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_confounds.tsv -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_desc-ImageQC_dwi.csv -sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_desc-SliceQC_dwi.json +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-ImageQC_dwi.csv +sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-SliceQC_dwi.json sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-brain_mask.nii.gz sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-eddy_cnr.nii.gz sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.b diff --git a/qsiprep/tests/data/intramodal_template_outputs.txt b/qsiprep/tests/data/intramodal_template_outputs.txt index a0d6ffce..3d599a9d 100644 --- a/qsiprep/tests/data/intramodal_template_outputs.txt +++ b/qsiprep/tests/data/intramodal_template_outputs.txt @@ -42,8 +42,8 @@ sub-tester/ses-1/anat sub-tester/ses-1/anat/sub-tester_ses-1_from-orig_to-anat_mode-image_xfm.txt sub-tester/ses-1/dwi sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_confounds.tsv -sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_desc-ImageQC_dwi.csv -sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_desc-SliceQC_dwi.json +sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-ImageQC_dwi.csv +sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-SliceQC_dwi.json sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-brain_mask.nii.gz sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-none_cnr.nii.gz sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-preproc_dwi.b @@ -55,8 +55,8 @@ sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_dwiref.nii.gz sub-tester/ses-2 sub-tester/ses-2/dwi sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_confounds.tsv -sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_desc-ImageQC_dwi.csv -sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_desc-SliceQC_dwi.json +sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-ImageQC_dwi.csv +sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-SliceQC_dwi.json sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-brain_mask.nii.gz sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-none_cnr.nii.gz sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b diff --git a/qsiprep/tests/data/maternal_brain_project_outputs.txt b/qsiprep/tests/data/maternal_brain_project_outputs.txt index 98389ff6..76390091 100644 --- a/qsiprep/tests/data/maternal_brain_project_outputs.txt +++ b/qsiprep/tests/data/maternal_brain_project_outputs.txt @@ -21,10 +21,10 @@ sub-01/ses-01/anat sub-01/ses-01/anat/sub-01_ses-01_rec-autobox_from-orig_to-anat_mode-image_xfm.txt sub-01/ses-01/dwi sub-01/ses-01/dwi/sub-01_ses-01_confounds.tsv -sub-01/ses-01/dwi/sub-01_ses-01_desc-ImageQC_dwi.csv -sub-01/ses-01/dwi/sub-01_ses-01_desc-SliceQC_dwi.json sub-01/ses-01/dwi/sub-01_ses-01_hmcOptimization.csv sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-3dSHORE_cnr.nii.gz +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-ImageQC_dwi.csv +sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-SliceQC_dwi.json sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-brain_mask.nii.gz sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.b sub-01/ses-01/dwi/sub-01_ses-01_space-ACPC_desc-preproc_dwi.b_table.txt diff --git a/qsiprep/workflows/dwi/finalize.py b/qsiprep/workflows/dwi/finalize.py index 0738a3a3..42c9bf0a 100644 --- a/qsiprep/workflows/dwi/finalize.py +++ b/qsiprep/workflows/dwi/finalize.py @@ -343,6 +343,7 @@ def init_dwi_finalize_wf( series_qc = pe.Node(SeriesQC(output_file_name=output_prefix), name="series_qc") ds_series_qc = pe.Node( DerivativesDataSink( + space="ACPC", desc="ImageQC", suffix="dwi", source_file=source_file, @@ -362,10 +363,10 @@ def init_dwi_finalize_wf( ) ds_merged_sidecar = pe.Node( DerivativesDataSink( - extension=".json", - source_file=source_file, space="ACPC", desc="preproc", + extension=".json", + source_file=source_file, base_directory=config.execution.output_dir, ), name="ds_merged_sidecar", @@ -376,6 +377,7 @@ def init_dwi_finalize_wf( # Write the carpetplot data (which is the text output from eddy) ds_carpetplot_data = pe.Node( DerivativesDataSink( + space="ACPC", desc="SliceQC", suffix="dwi", source_file=source_file, From af0d2083b9f6072a66cbbd60c26a7feacba292d4 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Tue, 12 Nov 2024 11:03:17 -0500 Subject: [PATCH 08/12] Update formatting of output file lists. --- docs/preprocessing.rst | 90 +++++++++++++++++++++++------------------- 1 file changed, 50 insertions(+), 40 deletions(-) diff --git a/docs/preprocessing.rst b/docs/preprocessing.rst index 844f8907..a70af536 100644 --- a/docs/preprocessing.rst +++ b/docs/preprocessing.rst @@ -233,42 +233,52 @@ written to ``/qsiprep/sub-/``. Derivatives related to anatomical files are nearly identical to those produced by ``fMRIprep`` and can be found in the ``anat`` subfolder. One major difference is that the anatomical derivatives are in LPS+ orientation and are realigned to the AC-PC, -while ``fMRIprep``'s are in RAS+ orientation and retain the original anatomical images' orientation. - -- ``_space-ACPC_desc-brain_mask.nii.gz`` Brain mask derived using ANTs' ``antsBrainExtraction.sh``. -- ``_space-ACPC_label-CSF_probseg.nii.gz`` -- ``_space-ACPC_label-GM_probseg.nii.gz`` -- ``_space-ACPC_label-WM_probseg.nii.gz`` tissue-probability maps. -- ``_space-ACPC_dseg.nii.gz`` Tissue class map derived using FAST. -- ``_space-ACPC_desc-preproc_T1w.nii.gz`` Bias field corrected T1w file, using ANTS' N4BiasFieldCorrection -- ``_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz`` Same as ``_brainmask`` above, but in MNI space. -- ``_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz`` -- ``_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz`` -- ``_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz`` Probability tissue maps, transformed into MNI space -- ``_space-MNI152NLin2009cAsym_dseg.nii.gz`` Same as ``_dtissue`` above, but in MNI space -- ``_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz`` Same as ``_preproc`` above, but in MNI space -- ``_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5`` Composite (warp and affine) transform to map from MNI to ACPC space -- ``_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5`` Composite (warp and affine) transform to transform ACPC into MNI space - -Derivatives related to diffusion images are in the ``dwi`` subfolder. - -- ``*_confounds.tsv`` A tab-separated value file with one column per calculated confound and one row per timepoint/volume - -Volumetric outputs are written out in ``ACPC`` space. - -- ``*dwiref.nii.gz`` The b0 template -- ``*desc-brain_mask.nii.gz`` The generous brain mask that should be reduced probably -- ``*desc-preproc_dwi.nii.gz`` Resampled DWI series including all b0 images. -- ``*desc-preproc_dwi.bval``, ``*desc-preproc_dwi.bvec`` FSL-style bvals and bvecs files. - *These will be incorrectly interpreted by MRTrix, but will work with DSI Studio and Dipy.* - Use the ``.b`` file for MRTrix. -- ``desc-preproc_dwi.b`` The gradient table to import data into MRTrix. This and the - ``_dwi.nii.gz`` can be converted directly to a ``.mif`` file using the ``mrconvert -grad _dwi.b`` - command. -- ``*bvecs.nii.gz`` Each voxel contains a gradient table that has been adjusted for local - rotations introduced by spatial warping. -- ``*cnr.nii.gz`` Each voxel contains a contrast-to-noise model defined as the variance of the - signal model divided by the variance of the error of the signal model. +while ``fMRIprep``'s are in RAS+ orientation and retain the original anatomical images' orientation :: + + sub-