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Looks like your setting for SUBJECTS_DIR together with the last 2 command line arguments,

tester  /mri/norm.mgz

- is causing it to look for the path $SUBJECTS_DIR/tester/mri/aseg.mgz - which does not exist.   Or I don’t see a directory $SUBJECTS_DIR/tester in the 7.3.2 release to read from and you cannot by default write to or create a new subdirectory ./tester under $SUBJECTS_DIR

Did you mean to set  SUBJECTS_DIR to something different where $SUBEJCTS_DIR/tester/mri/aseg.mgz already exists?  Maybe you need to change your command line arguments to be different.

- R.

On Oct 12, 2022, at 22:25, priya padma <priya@phenomx.ai> wrote:

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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 

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


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