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FSL is not included in the freesurfer distribution and is covered by its own license, i.e. for release 6, FMRIB Software Library, Release 6.0 (c) 2018, The University of Oxford.  It can be downloaded and installed from their wiki page, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation

If you install it on the same system(s) with the freesurfer installation, e.g., under /usr/local/fsl, then freesurfer should find that path autoamtically and set FSL_DIR to it when you setup the freesurfer environment.

You may however already have FSL installed on your servers in which case you can set FSL_DIR in your shell initialization file to point to that.  Subsequently, freesurfer should use that predefined setting for FSL_DIR when you start a new terminal window and display that setting of  FSL_DIR when you setup the freesurfer environment.

I think some people here may still use FSL version 5.0.7, but the latest version we have on hand is 6.0.6

- R.

On May 18, 2023, at 15:38, Lauren Stephens <laurenss@stanford.edu> wrote:

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Hi Freesurfers, 

I am trying to run tracula and was running the command bedpostx_datacheck and the terminal said: 

-------- freesurfer-darwin-macOS-7.3.2-20220804-6354275 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.3.2
FSFAST_HOME       /Applications/freesurfer/7.3.2/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/7.3.2/subjects
MNI_DIR           /Applications/freesurfer/7.3.2/mni
SLE-PBS-h4tkn18vq6x3:~ timothydurazzo$ bedpostx_datacheck
-bash: bedpostx_datacheck: command not found
SLE-PBS-h4tkn18vq6x3:~ timothydurazzo$ 

I see that FSL (FSL_DIR) is not in the freesurfer environment at the top, how can we add that in order to get bedpostx_datacheck to run properly? 

Thank you, 

Lauren Stephens, MS 
Assistant Clinical Research Coordinator 
Department of Psychiatry and Behavioral Science 
Stanford University School of Medicine  
P: (650)-725-1716

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