Summary of what happened:
Our subject identifiers that we push through Freesurfer are internal-only. We have a public-facing set of IDs, and we’d like to include anonymized Freesurfer data in the BIDS that we share. So: we need to take the stuff we have in $SUBJECT_DIR and transform it. Unfortunately, this isn’t as simple as just renaming the directories, as many of the outputs and logs include “# subjectname sub-XXXX” comments and cmdlines that include the subject name.
On the Freesurfer list, Douglas N. Greve said that one method might be:
# For mgz files, you can run
mri_convert --delete-cmds file.mgz file.mgz
# for surfaces, you can run the similar
mris_convert --delete-cmds lh.white lh.white
Command used (and if a helper script was used, a link to the helper script or the command generated):
mris_convert --delete-cmds original/sub-2001/surf/lh.pial test.pial
mris_info test.pial
This unfortunately still keeps the original “sub-2001” in the info output in a “file” line, note that the path is from the Singularity container mount that ran recon-all:
<snip>
z_(ras) : ( 0.0000, 1.0000, 0.0000)
c_(ras) : ( 0.5000, -6.0625, -33.2500)
file : /mnt/mr2m4/intermediate_data/freesurfer/sub-2001/mri/wm.mgz
Volume Geometry vox2ras
-1.00000 0.00000 0.00000 128.50000;
<snip>
and
mri_convert --delete-cmds original/sub-2001/mri/T1.mgz test.mgz
mri_info test.mgz
also still has the original “sub-2001” in its output:
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -6.0625
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -33.2500
talairach xfm : original/sub-2001/mri/transforms/talairach.xfm
Orientation : LIA
Version:
mris_convert freesurfer 7.4.1
Environment (Docker, Singularity / Apptainer, custom installation):
Custom installation of Freesurfer on Alma Linux 9
More information:
I have attempted to use nibabel’s freesurfer.read_geometry on .pial files, but that spits out ValueError: cannot reshape array of size 501062 into shape (3) and I’m definitely not smart enough to figure out what’s going on in the bowels of that function.