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rawdata is now sourcedata/raw, sometimes it's in the root but they don't make it clear when
…nventions - Updated mask file naming from 'seg-WM_DCE.nii' to 'label-WM_DCE.nii' in DCE_norm.py. - Adjusted file patterns and processing logic in VFA_norm.py to accommodate new mask naming. - Modified case_report.py to reflect changes in mask file names and added a function for space-RAS path conversion. - Updated ktrans_analysis.py to use 'label' prefixes for Ktrans files. - Changed max_disp.py to dynamically display the total number of frames. - Revised preprocess_all.sh to use 'label' suffixes for AIF masks and updated related file paths. - Ensured consistency in mask handling across scripts, including brain and tissue masks. - Updated documentation to reflect changes in file naming conventions for FreeSurfer parcellation.
…parallel jobs, new path search method, log autoAIF
Co-authored-by: lsaca05 <46550669+lsaca05@users.noreply.github.com>
Co-authored-by: lsaca05 <46550669+lsaca05@users.noreply.github.com>
… ROCKETSHIP and GPUFIT paths, streamline preprocessing, and update documentation for clarity.
…dling, and update output file naming conventions to include gzip compression.
…rd cuts, fix caserep aif NaNs, fix rawdata->sourcedata/raw refs, fix a couple other naming changes, fix exclude sheet key diffs
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