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
 

        External Email - Use Caution        

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 

PhenoMx, Inc.
priya@phenomx.ai | (+82)10-5405-2685