From 399c7bd9bfbd8e85afb0ed24e1dfba095c7ced4e Mon Sep 17 00:00:00 2001 From: Ian-Goodall-Halliwell <90027009+Ian-Goodall-Halliwell@users.noreply.github.com> Date: Wed, 4 Dec 2024 13:16:00 -0500 Subject: [PATCH 1/2] Cleaning changes --- .gitignore | 3 ++- surf2vol.bat | 26 -------------------------- 2 files changed, 2 insertions(+), 27 deletions(-) delete mode 100644 surf2vol.bat diff --git a/.gitignore b/.gitignore index e95db1b..130a81c 100644 --- a/.gitignore +++ b/.gitignore @@ -7,4 +7,5 @@ run.* *.bat *.bash .vscode -.pytest_cache/ \ No newline at end of file +.pytest_cache/ +/run.bat \ No newline at end of file diff --git a/surf2vol.bat b/surf2vol.bat deleted file mode 100644 index c3c23c4..0000000 --- a/surf2vol.bat +++ /dev/null @@ -1,26 +0,0 @@ -wb_command -metric-resample^ - "C:\Users\Ian\Documents\GitHub\z-brains-IanTesting\src\data\sub-PX001_ses-02_hemi-L_surf-fsLR-32k_label-midthickness_feature-FA_smooth-10mm_analysis-asymmetry.func.gii"^ - "C:\Users\Ian\Documents\GitHub\z-brains-IanTesting\src\data\templates\fsLR-32k.L.sphere.reg.surf.gii"^ - "E:\data\derivatives\micapipe\sub-PX001\ses-02\surf\sub-PX001_ses-02_hemi-L_surf-fsnative_label-sphere.surf.gii"^ - "BARYCENTRIC"^ - "C:\Users\Ian\Documents\GitHub\z-brains-IanTesting\src\data\fsnative_surf_L.func.gii" - -wb_command -metric-to-volume-mapping^ - "C:\Users\Ian\Documents\GitHub\z-brains-IanTesting\src\data\fsnative_surf_L.func.gii"^ - "E:\data\derivatives\micapipe\sub-PX001\ses-02\surf\sub-PX001_ses-02_hemi-L_space-nativepro_surf-fsnative_label-midthickness.surf.gii"^ - "C:\Users\Ian\Documents\GitHub\z-brains-IanTesting\src\data\patient_surfs\sub-PX001_ses-02_space-nativepro_map-T1map.nii.gz"^ - "C:\Users\Ian\Documents\GitHub\z-brains-IanTesting\src\data\Nativepro_L.nii.gz"^ - -ribbon-constrained^ - "E:\data\derivatives\micapipe\sub-PX001\ses-02\surf\sub-PX001_ses-02_hemi-L_space-nativepro_surf-fsnative_label-white.surf.gii"^ - "E:\data\derivatives\micapipe\sub-PX001\ses-02\surf\sub-PX001_ses-02_hemi-L_space-nativepro_surf-fsnative_label-pial.surf.gii" - -@REM wb_command -volume-resample^ -@REM "C:\Users\Ian\Documents\GitHub\z-brains-IanTesting\src\data\Nativepro_L.nii.gz"^ -@REM "C:\Users\Ian\Documents\GitHub\z-brains-IanTesting\src\data\templates\MNI152_T1_0.8mm_brain.nii.gz"^ -@REM ENCLOSING_VOXEL^ -@REM "C:\Users\Ian\Documents\GitHub\z-brains-IanTesting\src\data\warpthenaffine.nii.gz"^ -@REM -warp^ -@REM "E:\data\derivatives\micapipe\sub-PX001\ses-02\xfm\sub-PX001_ses-02_from-nativepro_brain_to-MNI152_0.8mm_mode-image_desc-SyN_1Warp.nii.gz"^ -@REM -affine^ -@REM "C:\Users\Ian\Documents\GitHub\z-brains-IanTesting\src\data\transforms\canonical_to_fsaverage_noninv.txt" - From ff26264f2a6b3ef86b6b518b5d81d185adf4c745 Mon Sep 17 00:00:00 2001 From: Ian-Goodall-Halliwell <90027009+Ian-Goodall-Halliwell@users.noreply.github.com> Date: Wed, 4 Dec 2024 13:17:28 -0500 Subject: [PATCH 2/2] Delete run.bat --- run.bat | 34 ---------------------------------- 1 file changed, 34 deletions(-) delete mode 100644 run.bat diff --git a/run.bat b/run.bat deleted file mode 100644 index 5b7ca1b..0000000 --- a/run.bat +++ /dev/null @@ -1,34 +0,0 @@ -setlocal enabledelayedexpansion -set "pth_dataset=E:\data" - -set "micapipe_dir=micapipe" -set "hippunfold_dir=hippunfold" -set "zbrains_dir=zbrains_vol2" - -set "demo_controls=E:\participants_mics_hc.csv" -set "demo_patients=E:\PX_participants.csv" - -set "sids=sub-PX002" -set "sess=all" -call conda activate zbrains -call python -m src.zbrains --run "analysis" ^ - --sub "%sids%" ^ - --micapipe %micapipe_dir% ^ - --hippunfold %hippunfold_dir% ^ - --dataset %pth_dataset% ^ - --zbrains %zbrains_dir% ^ - --demo_ref %demo_controls% ^ - --demo %demo_patients% ^ - --dataset_ref %pth_dataset% ^ - --zbrains_ref %zbrains_dir% ^ - --smooth_ctx 10 ^ - --smooth_hip 5 ^ - --n_jobs 4 ^ - --n_jobs_wb 4 ^ - --dicoms 0 ^ - --label_ctx "white" ^ - --wb_path "C:/Users/Ian/Downloads/workbench-windows64-v1.5.0/workbench/bin_windows64" ^ - --column_map participant_id=ID session_id=SES ^ - --verbose 2 - ) -pause \ No newline at end of file