Hi Padma,
It can't find the file: /Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz
Are you trying to run this on a subject called sub-AD003S1059S61129? If so, can you try:
mri_compute_volume_fractions --o test --regheader sub-AD003S1059S61129 /mri/norm.mgz
-Paul
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of priya padma priya@phenomx.ai Sent: Wednesday, October 12, 2022 10:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mghread : cannot open the file
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Hello Team,
I am trying to find the volume of WM, GM, CSF separately and I came across this command namely "mri_compute_volume_fractions"
Looking through all the email archives I gave the following line as the command after setting the paths
$ mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz
but I get the following error
user-MacBook-Pro:sub-AD003S1059S61129 user$ mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz
supposed to be reproducible but seed not set
7.3.2
sysname Darwin
hostname user-MacBook-Pro.local
machine x86_64
user <username>
setenv SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjects
cd /Applications/freesurfer/7.3.2/subjects/sub-AD003S1059S61129
mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz
outstem test
regfile (null)
regtype 0
segfile aseg.mgz
wsurf white
psurf pial
TempVolFile /mri/norm.mgz
USF 2
Reading in aseg and surfs from /Applications/freesurfer/7.3.2/subjects/tester
Loading /Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz
error: mghRead(/Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz, -1): could not open file
I set all the paths so why am I not able to read the mgz file?
Could anyone help me with this ?
Thank you
-- Best Regards Padma Priya AI Developer [https://secure-web.cisco.com/1Sii6Tv7lFwUl5uVc4ILyhApqN4giKhqzdQnct79ykzdW_z...] PhenoMx, Inc. priya@phenomx.aimailto:priya@phenomx.ai | (+82)10-5405-2685