External Email - Use Caution
Can you try to source your Freesurfer environment?
For tcsh or csh,
setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
For bash,
export FREESURFER_HOME=<freesurfer_installation_directory>/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of K Eswar
Sent: Monday, October 9, 2023 1:59 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_synth functions errors
External Email - Use Caution
Hello Freesurfer Developers,
I am attempting to process mri_synthseg,mri_synthsr,mri_synthstrip and it shows
the following error
For mri_synthseg and mri_synthsr:
Traceback (most recent call last):
File "/home/sgbc/freesurfer/python/scripts/mri_synthseg", line 10, in <module>
import surfa as sf
ModuleNotFoundError: No module named 'surfa'
For mri_synthstrip
Traceback (most recent call last):
File "/home/sgbc/freesurfer/python/scripts/mri_synthstrip", line 5, in
<module>
import torch
ModuleNotFoundError: No module named 'torch'
I am using linux operating system_Ubuntu 22.04.2 LTS
I have recently installed infant freesurfer and I don't know if the problem is
following to it as I expect path might have been changed
I tried looking for these errors in the forum, however I did not find the fix.
Thank you for your time and consideration
Kind regards
K Eswar
Project scientist
Sudha Gopalakrishnan Brain Centre
IIT Madras, India
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