Hi Padma,
The error is saying it can't find the file /mri/norm.mgz. Does that file exist? What does `ls /mri/norm.mgz` return?
-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 19, 2022 2:07 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mghread : cannot open the file
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Hello Team,
Is there any solution for the above mentioned issue? I am still struck in the same place.
Thank you
On Fri, Oct 14, 2022 at 10:20 AM priya padma <priya@phenomx.aimailto:priya@phenomx.ai> wrote: 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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of priya padma <priya@phenomx.aimailto:priya@phenomx.ai> Sent: Wednesday, October 12, 2022 10:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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
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-- Cheers Priya
-- Cheers Priya