====== Freesurfer for BrainMechR01 (7T) ======

As of 2025-04-01 [[:tools:freesurfer]] has been run at least 3 times on the [[:grants:7t]]'s [[:grants:7t:mr:anat]] data. 
Due to scanner stability issues, not every visit has a higher quality ''MP2RAGE'' acquisition. Some visits only have the safer-for-the-scanner faster/lower quality ''mprage'' acquisition. Some visits have both anatomical acquisitions.

  * ''FS7.4.1_long'' (2023) is the most recent and the only run to include Val's ''UNIDENT1corrected''. Run by VS in singularity  ([[:projects:mtrsnr]]).
    * ''/Volumes/Hera/preproc/7TBrainMech_rest/FS7.4.1_long/sub-10129_ses-20180917.long.sub-10129''
  * ''FS7.2'' (2021) was run with the original MP2RAGE input. first version to include [[:brain:hippocampus]] segmentation "HBT"
    * ''/Volumes/Hera/preproc/7TBrainMech_rest/FS7.2/highres/10129_20180917/''
  * ''FS'' (2018) is ''freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c'' run on [[:tools:PSC]] (with ''pylon'' before the switch to ''ocean'')
    * ''/Volumes/Hera/preproc/7TBrainMech_rest/FS/10129_20180917/''

===== Don't Mix versions =====

For example, FS6 ''%%mri-binarize --wm aseg.mgz%%'' will not overlap with HBT from FS7.2 but the gm mask extracted from ''FS7.2/aseg.mgz'' will.


{{:grants:7t:mr:pasted:20250401-173146.png?150}}
===== Metadata/Provenance =====
''find'' and ''grep'' on the output log (''scripts/recon-all.log'') can show finish date (of example participant ''10129'') and run parameters (including input file)

<code>
find /Volumes/Hera/preproc/7TBrainMech*/FS*/{,*/}*10129*/scripts/recon-all.log -printf "%TF %p\n"|sort -nr

2023-12-18 /Volumes/Hera/preproc/7TBrainMech_rest/FS7.4.1_long/sub-10129_ses-20180917/scripts/recon-all.log
2023-12-18 /Volumes/Hera/preproc/7TBrainMech_rest/FS7.4.1_long/sub-10129_ses-20180917.long.sub-10129/scripts/recon-all.log
2023-12-18 /Volumes/Hera/preproc/7TBrainMech_rest/FS7.4.1_long/sub-10129/scripts/recon-all.log
2021-12-15 /Volumes/Hera/preproc/7TBrainMech_rest/FS7.2/highres/10129_20180917/scripts/recon-all.log
2018-12-04 /Volumes/Hera/preproc/7TBrainMech_rest/FS/10129/scripts/recon-all.log
2018-12-04 /Volumes/Hera/preproc/7TBrainMech_rest/FS/10129_20180917/scripts/recon-all.l
</code>

<code>
grep '\-all.*nii' /Volumes/Hera/preproc/7TBrainMech*/FS*/{,*/}*10129*/scripts/recon-all.log 

/Volumes/Hera/preproc/7TBrainMech_rest/FS/10129_20180917/scripts/recon-all.log:
  -all -s 10129 -i /pylon5/db5fp7p/luna/T1/sub-10129/20180917/anat/sub-10129_T1w.nii.gz

/Volumes/Hera/preproc/7TBrainMech_rest/FS/10129/scripts/recon-all.log:
  -all -s 10129 -i /pylon5/db5fp7p/luna/T1/sub-10129/20180917/anat/sub-10129_T1w.nii.gz

/Volumes/Hera/preproc/7TBrainMech_rest/FS7.2/highres/10129_20180917/scripts/recon-all.log:
 /opt/ni_tools/freesurfer7.2//bin/recon-all -subjid 10129_20180917 -i /Volumes/Hera/Projects/7TBrainMech/BIDS//sub-10129/20180917/anat/sub-10129_T1w.nii.gz -all -cm

/Volumes/Hera/preproc/7TBrainMech_rest/FS7.4.1_long/sub-10129_ses-20180917/scripts/recon-all.log:
  /opt/freesurfer/bin/recon-all -subjid sub-10129_ses-20180917 -sd /Freesurfer_output -3T -i /BIDS/sub-10129/ses-20180917/anat/sub-10129_ses-20180917_acq-UNIDENT1corrected_T1w.nii.gz -all -openmp 2
  
</code>