External Email - Use Caution
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.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.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 CautionHello 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 priya@phenomx.ai | (+82)10-5405-2685*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1D1ZejX1HeZIQWWaocgjn4-M5XHWQDYpHCeasEzatHm8CkP... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1CA2hhj6nFpfQpt_iq46xX2heLD4WiiZkoZSRPjFb3a_QLo... < https://secure-web.cisco.com/1CA2hhj6nFpfQpt_iq46xX2heLD4WiiZkoZSRPjFb3a_QLo... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
-- Cheers Priya