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grants:spa:anatomical [2026/08/24 18:19] – vsydnorgrants:spa:anatomical [2026/08/24 18:33] (current) – vsydnor
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   * SPM UNICORT is run with default parameters. The unicort script called is Hera/Projects/SPA/scripts/mri/preproc/spm_unicort.m   * SPM UNICORT is run with default parameters. The unicort script called is Hera/Projects/SPA/scripts/mri/preproc/spm_unicort.m
  
-3. Run ''Hera/Projects/SPA/scripts/mri/preproc/02_fs.bash'' to run freesurfer on denoised and unicort corrected UNI images. The output is Hera/Projects/SPA/scripts/mri/fs/7.4.1-denunicort-hires+3. Run ''Hera/Projects/SPA/scripts/mri/preproc/02_fs.bash'' to run freesurfer on denoised and unicort corrected UNI images. The output is Hera/Projects/SPA/scripts/mri/fs/8.2.0
  
-  * Freesurfer is run via docker container. We are using freesurfer version 7.4.1 with the -hires flag and running cross-sectional (not longitudinal) recon-all. The main recon-all call is recon-all -hires -all -i "$f" -s "$sub". Note: some segmentations are very bad with 7.4.1 when the cerebellum is cut off. We are testing freesurfer 8 (with syntheseg) to see if this improves it+  * Freesurfer is run via docker container. We are using freesurfer version 8.2.0 with the -hires flag and running cross-sectional (not longitudinal) recon-all. The main recon-all call is recon-all -hires -all -i "$f" -s "$sub". 
   * Input to freesurfer is the denoised and unicort-corrected UNI from above (msub-$_ses-$_DEN-10.nii) (INPUTS=(../fs/bids-t1only/sub-/ses-/anat/msub-_ses-_DEN-10.nii) ||   * Input to freesurfer is the denoised and unicort-corrected UNI from above (msub-$_ses-$_DEN-10.nii) (INPUTS=(../fs/bids-t1only/sub-/ses-/anat/msub-_ses-_DEN-10.nii) ||
  
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 <code -> <code ->
 bids_anat()  { find Hera/Raw/BIDS/SPA/sub-*/ses-*/anat -iname '*UNIT1*'; } bids_anat()  { find Hera/Raw/BIDS/SPA/sub-*/ses-*/anat -iname '*UNIT1*'; }
-ls_reconlog(){ ls Hera/Projects/SPA/scripts/mri/fs/7.4.1-denunicort-hires/ses-*/sub-*/scripts/recon-all.done; }+ls_reconlog(){ ls Hera/Projects/SPA/scripts/mri/fs/8.2.0/ses-*/sub-*/scripts/recon-all.done; }
  
 comm -23 \ comm -23 \