This can be a little tricky. Some information gets embedded into the
files (you won't find this with a text search). You can generally see it
with mri_info (mgz files) or mris_info (surface files)
However, mri_info can print out info that is not in the file but just
relates to the location of the file. Eg, it prints out the "transform
name". Eg, if you run mri_info orig.mgz you will see something like
/autofs/vast/adni3/subjects/002_S_4654.y0/mri/transforms/talairach.xfm
This gives the impression that this information is in the file, but it
is not. If you copy orig.mgz to somewhere else and run mri_info, you
will not see a transform name. mri_info is actually just finding the
talairach.xfm file under the transform folder.
So if you just copy your subject to another folder, the new folder will
appear in the transform name
If you run mris_info lh.white, you will see something like
file : /autofs/vast/adni3/subjects/002_S_4654.y0/mri/wm.mgz
This info is embedded in the surface file. To change it, you can run
something like
mris_convert --vol-geom ../mri/wm.mgz lh.white lh.white
Some of the info is that command lines can get embedded into files. 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 # can be combined with
--vol-geom above
So, my strategy would be to copy your subject folder to a new folder,
the run mri_convert and mris_convert as above, then go through each file
running mri_info or mris_info and looking for your original subject name.
For defacing, you can use https://surfer.nmr.mgh.harvard.edu/fswiki/MiDeFace
On 6/18/2024 12:43 PM, Dan Fitch wrote:
External Email - Use Caution
Hi folks,
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.
1.
Is there an extant method to rename subject directories? I've
searched around on Github and on this list's archives; came up blank.
2.
Would it be enough to walk the directories and replace all
instances of e.g. "sub-1234" with "sub-30000"? Or do subject
numbers get embedded in binary headers/metadata, as well?
The extra-fun touch is that we are not actually allowed to SEE the
mapping from internal IDs to public-facing IDs, so any tool we provide
for this translation needs to be useable by someone who is unfamiliar
with Freesurfer. (Don't ask.)
Then we will also need to de-face all the images, of course.
Any tips or leads appreciated; otherwise, I'll build a thing and
eventually post about it here.
Dan Fitch
Research Engineer
University of Wisconsin-Madison Institute on Aging
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