Freesurfer for BrainMechR01 (7T)

As of 2025-04-01 freesurfer has been run at least 3 times on the Brain Mechanisms R01 (7T)'s 7T Anatomical Acquisitions data. Due to scanner stability issues, not every visit has a higher quality MP2RAGE (+UNICORT) 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 (Harnessing Quantitative MRI to Map Developmental Increases in Intracortical Myelin and their Biobehavioral Consequences) on Pittsburgh Super Computer.
- /Volumes/Hera/preproc/7TBrainMech_rest/FS7.4.1_long/sub-10129_ses-20180917.long.sub-10129
- syncing, see /Volumes/Hera/preproc/7TBrainMech_rest/FS7.4.1_long/psc_sync.bash (reran 2025-10-21 for SM).
FS7.2 (2021) was run with the original MP2RAGE input. first version to include 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 Pittsburgh Super Computer (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.

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)

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

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