Edit

CBICA · Sep 11, 2024 · 1cd3922 · 1cd3922
1 parent 1ba4793
commit 1cd3922
Show file tree

Hide file tree

Showing 61 changed files with 9 additions and 15,685 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -1,8 +1,7 @@
 # NiChart packages
-NiChart-Viewer-Demo
 spare-scores
 NiChartHarmonize
-NiChart_DLMUSE
+#NiChart_DLMUSE
 
 # general python dependencies
 argparse
@@ -15,6 +14,7 @@ sphinx
 
 
 # streamlit
+st_pages==1.0.1
 streamlit_plotly_events
 Jinja2
 plotly-express
diff --git a/src/Harmonization/ComBatFam_Pipeline b/src/Harmonization/ComBatFam_Pipeline
diff --git a/src/Image_Processing/DTI/qsiprep b/src/Image_Processing/DTI/qsiprep
diff --git a/src/Image_Processing/fMRI/fmriprep b/src/Image_Processing/fMRI/fmriprep
diff --git a/src/Image_Processing/fMRI/xcp_d b/src/Image_Processing/fMRI/xcp_d
diff --git a/src/Image_Processing/sMRI/SOPNMF b/src/Image_Processing/sMRI/SOPNMF
diff --git a/src/Machine_Learning/SurrealGAN b/src/Machine_Learning/SurrealGAN
diff --git a/src/Machine_Learning/spare_score b/src/Machine_Learning/spare_score
diff --git a/src/workflow/test_input/vTest1/Study1/filtered_data/Study1_DLMUSE_raw.csv b/src/workflow/test_input/vTest1/Study1/filtered_data/Study1_DLMUSE_raw.csv
diff --git a/src/workflow/test_input/vTest1/Study1/out_combat/Study1_DLMUSE_raw_COMBAT_all.csv b/src/workflow/test_input/vTest1/Study1/out_combat/Study1_DLMUSE_raw_COMBAT_all.csv
diff --git a/src/workflow/test_input/vTest1/Study1/out_combat/Study1_DLMUSE_raw_COMBAT_single.csv b/src/workflow/test_input/vTest1/Study1/out_combat/Study1_DLMUSE_raw_COMBAT_single.csv
diff --git a/src/workflow/test_input/vTest1/Study1/out_combined/Study1_DLMUSE_All.csv b/src/workflow/test_input/vTest1/Study1/out_combined/Study1_DLMUSE_All.csv
diff --git a/src/workflow/test_input/vTest1/Study1/out_rois/Study1_DLMUSE_normICV.csv b/src/workflow/test_input/vTest1/Study1/out_rois/Study1_DLMUSE_normICV.csv
diff --git a/src/workflow/test_input/vTest1/Study1/out_rois/Study1_DLMUSE_raw.csv b/src/workflow/test_input/vTest1/Study1/out_rois/Study1_DLMUSE_raw.csv
diff --git a/src/workflow/test_input/vTest1/Study1/out_spare/Study1_DLMUSE_raw_COMBAT_SPARE-Scores.csv b/src/workflow/test_input/vTest1/Study1/out_spare/Study1_DLMUSE_raw_COMBAT_SPARE-Scores.csv
diff --git a/src/workflow/test_input/vTest1/flag_VIEWED.csv b/src/workflow/test_input/vTest1/flag_VIEWED.csv
diff --git a/src/workflow/test_output/Study1/filtered_data/Study1_DLMUSE_raw.csv b/src/workflow/test_output/Study1/filtered_data/Study1_DLMUSE_raw.csv
diff --git a/src/workflow/test_output/Study1/out_combat/Study1_DLMUSE_raw_COMBAT_all.csv b/src/workflow/test_output/Study1/out_combat/Study1_DLMUSE_raw_COMBAT_all.csv
diff --git a/src/workflow/test_output/Study1/out_combat/Study1_DLMUSE_raw_COMBAT_single.csv b/src/workflow/test_output/Study1/out_combat/Study1_DLMUSE_raw_COMBAT_single.csv
diff --git a/src/workflow/test_output/Study1/out_combined/Study1_DLMUSE_All.csv b/src/workflow/test_output/Study1/out_combined/Study1_DLMUSE_All.csv
diff --git a/src/workflow/test_output/Study1/out_rois/Study1_DLMUSE_normICV.csv b/src/workflow/test_output/Study1/out_rois/Study1_DLMUSE_normICV.csv
diff --git a/src/workflow/test_output/Study1/out_rois/Study1_DLMUSE_raw.csv b/src/workflow/test_output/Study1/out_rois/Study1_DLMUSE_raw.csv
diff --git a/src/workflow/test_output/Study1/out_spare/Study1_DLMUSE_raw_COMBAT_SPARE-Scores.csv b/src/workflow/test_output/Study1/out_spare/Study1_DLMUSE_raw_COMBAT_SPARE-Scores.csv
diff --git a/src/workflow/test_output/flag_VIEWED.csv b/src/workflow/test_output/flag_VIEWED.csv
diff --git a/src/workflow/test_output/vTest1/Study1/filtered_data/Study1_DLMUSE_raw.csv b/src/workflow/test_output/vTest1/Study1/filtered_data/Study1_DLMUSE_raw.csv
diff --git a/src/workflow/test_output/vTest1/Study1/out_combat/Study1_DLMUSE_raw_COMBAT_all.csv b/src/workflow/test_output/vTest1/Study1/out_combat/Study1_DLMUSE_raw_COMBAT_all.csv
diff --git a/src/workflow/test_output/vTest1/Study1/out_combined/Study1_DLMUSE_All.csv b/src/workflow/test_output/vTest1/Study1/out_combined/Study1_DLMUSE_All.csv
diff --git a/src/workflow/test_output/vTest1/Study1/out_rois/Study1_DLMUSE_normICV.csv b/src/workflow/test_output/vTest1/Study1/out_rois/Study1_DLMUSE_normICV.csv
diff --git a/src/workflow/test_output/vTest1/Study1/out_rois/Study1_DLMUSE_raw.csv b/src/workflow/test_output/vTest1/Study1/out_rois/Study1_DLMUSE_raw.csv
diff --git a/src/workflow/test_output/vTest1/Study1/out_spare/Study1_DLMUSE_raw_COMBAT_SPARE-Scores.csv b/src/workflow/test_output/vTest1/Study1/out_spare/Study1_DLMUSE_raw_COMBAT_SPARE-Scores.csv
diff --git a/src/workflow/test_output/vTest1/config/config.yaml b/src/workflow/test_output/vTest1/config/config.yaml
diff --git a/src/workflow/test_output/vTest1/flag_VIEWED.csv b/src/workflow/test_output/vTest1/flag_VIEWED.csv
diff --git a/src/workflow/test_output/vTest2/Study1/dlmuse/tmprun_dlmuse/nnUNet_model b/src/workflow/test_output/vTest2/Study1/dlmuse/tmprun_dlmuse/nnUNet_model
diff --git a/...rkflow/test_output/vTest2/Study1/dlmuse/tmprun_dlmuse/nnUNet_out/out_dlicv_mask/plans.pkl b/...rkflow/test_output/vTest2/Study1/dlmuse/tmprun_dlmuse/nnUNet_out/out_dlicv_mask/plans.pkl
diff --git a/.../vTest2/Study1/dlmuse/tmprun_dlmuse/nnUNet_out/out_to_LPS/IXI002-Guys-0828_T1_0000.nii.gz b/.../vTest2/Study1/dlmuse/tmprun_dlmuse/nnUNet_out/out_to_LPS/IXI002-Guys-0828_T1_0000.nii.gz
diff --git a/...ut/vTest2/Study1/dlmuse/tmprun_dlmuse/nnUNet_out/out_to_LPS/IXI012-HH-1211_T1_0000.nii.gz b/...ut/vTest2/Study1/dlmuse/tmprun_dlmuse/nnUNet_out/out_to_LPS/IXI012-HH-1211_T1_0000.nii.gz
diff --git a/...ut/vTest2/Study1/dlmuse/tmprun_dlmuse/nnUNet_out/out_to_LPS/IXI013-HH-1212_T1_0000.nii.gz b/...ut/vTest2/Study1/dlmuse/tmprun_dlmuse/nnUNet_out/out_to_LPS/IXI013-HH-1212_T1_0000.nii.gz
+135 −86		.circleci/config.yml
+0 −3		.circleci/pytests/test_drbuddi.py
+5 −4		Dockerfile
+0 −71		docker/files/neurodebian.gpg
+0 −50		docker/scripts/get_templates.sh
+0 −2		pyproject.toml
+0 −30		qsiprep/data/boilerplate.bib
+3 −3		qsiprep/data/intramodal_ACPC_sloppy.json
+24 −20		qsiprep/interfaces/anatomical.py
+55 −0		qsiprep/interfaces/freesurfer.py
+6 −1		qsiprep/interfaces/images.py
+1 −1		qsiprep/interfaces/tortoise.py
+38 −12		qsiprep/tests/test_cli.py
+26 −10		qsiprep/workflows/anatomical/volume.py
+8 −3		qsiprep/workflows/dwi/hmc.py
+6 −1		qsiprep/workflows/dwi/hmc_sdc.py
+2 −1		qsiprep/workflows/dwi/resampling.py
+2 −2		CITATION.cff
+27 −0		docs/changes.md
+1 −2		docs/outputs.rst
+0 −3		docs/usage.rst
+2 −3		docs/workflows.rst
+1 −1		xcp_d/cli/parser.py
+0 −10		xcp_d/data/io_spec.yaml
+0 −7		xcp_d/ingression/ukbiobank.py
+0 −1		xcp_d/ingression/utils.py
+0 −14		xcp_d/interfaces/utils.py
+0 −5		xcp_d/tests/conftest.py
+0 −1		xcp_d/tests/data/test_ds001419_cifti_outputs.txt
+0 −1		xcp_d/tests/data/test_ds001419_nifti_outputs.txt
+0 −1		xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt
+0 −1		xcp_d/tests/data/test_nibabies_outputs.txt
+0 −1		xcp_d/tests/data/test_pnc_cifti_outputs.txt
+0 −1		xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt
+0 −1		xcp_d/tests/data/test_ukbiobank_outputs.txt
+2 −0		xcp_d/tests/test_cli.py
+2 −1		xcp_d/tests/test_cli_run.py
+0 −5		xcp_d/tests/test_workflows_anatomical.py
+3 −9		xcp_d/utils/bids.py
+2 −41		xcp_d/workflows/anatomical/volume.py
+1 −4		xcp_d/workflows/base.py
+15 −0		CITATION.cff
+1 −1		LICENSE
+10 −7		README.md
+ −		data/atlas/MuSIC.tar.xz
+10 −2		docs/index.md
+2 −2		setup.py
+2 −2		sopnmf/base.py
+1 −1		sopnmf/main.py
+2 −2		sopnmf/opnmf_core.py
+2 −2		sopnmf/opnmf_post.py
+2 −2		sopnmf/utils.py
+2 −2		sopnmf/workflow.py
+0 −19		.pre-commit-config.yaml
+133 −234		SurrealGAN/Surreal_GAN_representation_learning.py
+20 −27		SurrealGAN/copula.py
+34 −57		SurrealGAN/data_loading.py
+267 −386		SurrealGAN/model.py
+20 −17		SurrealGAN/modules.py
+49 −70		SurrealGAN/networks.py
+164 −299		SurrealGAN/training.py
+177 −286		SurrealGAN/utils.py
+19 −31		datasets/sample_code.py
+13 −30		pretrained_models/brain_aging_5rindices/apply_pretained_model.py
+0 −41		setup.cfg
+12 −11		setup.py
+24 −0		.github/workflows/macos-tests-3.12.yml
+1 −1		.github/workflows/macos-tests-3.8.yml
+4 −12		.github/workflows/ubuntu-tests-3.12.yml
+3 −13		.github/workflows/ubuntu-tests-3.8.yml
+0 −33		.github/workflows/ubuntu_test_cases_p3-12.yml
+4 −2		README.md
+6 −7		requirements.txt
+1 −1		setup.cfg
+3 −3		spare_scores/mlp.py
+12 −10		spare_scores/mlp_torch.py
+7 −2		spare_scores/svm.py
+0 −0		test_data_prep.py