Hello Rana,

Running that script (or any other freesurfer commands/binaries) assumes you’ve setup the freesurfer environment by,

1) setting FREESURFER_HOME in your shell to point to the top of the freesurfer tree

2) source’ing a shell init file to set PATH and other environment variables in order to run freesurfer commands

There is info on the wiki about this for linux,

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- and the Mac,

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Just find the absolute path to the top of the freesurfer tree. For the latest 7.2.0 release installed by the package installers the version number is already in the absolute pathname to the top of the freesurfer tree. On linux that path would be /usr/local/freesurfer/7.2.0 and on the Mac that path would be /Applications/freesurfer/7.2.0

For that linux path using bash you would do,

$ bash

$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0

$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

When you run the source command to read the SetUpFreeSurfer script for the shell you are using, the version of freesurfer will get printed out automatically for you.

Using the 7.2.0 linux release you would see the string between the dashes no matter what the absolute path is to FREESURFER_HOME on your system.

tmp$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0

tmp$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

-------- freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b --------

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /usr/local/freesurfer/7.2.0

FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR      /usr/local/freesurfer/7.2.0/subjects

MNI_DIR           /usr/local/freesurfer/7.2.0/mni

FSL_DIR           /usr/pubsw/packages/fsl/current

… now run any freesurfer commands …

- R

On Sep 22, 2021, at 18:04, Banik, Rana <rana.banik@vanderbilt.edu> wrote:
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External Email - Use Caution

Running freesurfer from terminal with the following error:
banikr2@banikr:~/freesurfer/bin$ ./freesurfer 

FreeSurfer is a set of tools for the analysis and visualization
of structural and functional brain imaging data. FreeSurfer
also refers to the structural imaging stream within the
FreeSurfer suite.

Users should consult the online documentation available at:

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Alternatively, the 'recon-all' command help-text provides
adequate information to begin processing subject data, such
as the sample subject 'bert' found in the 'freesurfer/subjects'
directory.  Type 'recon-all --help' to view this help-text.

Direct comments and questions to:

  freesurfer@nmr.mgh.harvard.edu

You are running this version of FreeSurfer:

cat: /build-stamp.txt: No such file or directory
Any idea what went wrong or how to fix it?

Rana Banik
Graduate Student
Dept. of Biomedical Engineering
Vanderbilt University, Nashville, TN

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