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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

 

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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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