Hi Paul,

Thank you for your email. I tried how to told me

"mri_compute_volume_fractions --o test --regheader sub-AD003S1059S61129_0000 /mri/norm.mgz"

I gave this command, initially it used to give the error in the starting when it tries to load aseg,mgz file but now it shows error after few steps

~/Priya/freesurfer/subjects$ mri_compute_volume_fractions --o test --regheader sub-AD003S1059S61129_0000 /mri/norm.mgz
mri_compute_vol supposed to be reproducible but seed not set

7.3.2
sysname Linux
hostname ai01
machine x86_64
user phenomx
setenv SUBJECTS_DIR /home/phenomx/Priya/freesurfer/subjects
cd /home/phenomx/Priya/freesurfer/subjects
mri_compute_volume_fractions --o test --regheader sub-AD003S1059S61129_0000 /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 /home/phenomx/Priya/freesurfer/subjects/sub-AD003S1059S61129_0000
Loading /home/phenomx/Priya/freesurfer/subjects/sub-AD003S1059S61129_0000/mri/aseg.mgz
Filling empty voxels with extracerebral CSF (if not there already), nDil=3
Loading orig /home/phenomx/Priya/freesurfer/subjects/sub-AD003S1059S61129_0000/mri/orig.mgz
Loading template /mri/norm.mgz
error: mghRead(/mri/norm.mgz, -1): could not open file

If I am not wrong, I believe the search is not directed to the right path, but when everything is right I donno how to solve this. Is there any solution ?

Thank you

On Fri, Oct 14, 2022 at 12:54 AM Wighton, Paul <PWIGHTON@mgh.harvard.edu> wrote:

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

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