Add space-ACPC to QC files.

PennLINC · Nov 12, 2024 · 42d7c04 · 42d7c04
1 parent d4286d5
commit 42d7c04
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Showing 16 changed files with 38 additions and 36 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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,