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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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