External Email - Use Caution
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, https://secure-web.cisco.com/16O3UT_MWu0a4Jy2ifmfNIL0rCFkh8zn4r296wgn0isZ8kQ... 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: External Email - Use Caution 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/7.3.2FSFAST_HOME /Applications/freesurfer/7.3.2/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Applications/freesurfer/7.3.2/subjectsMNI_DIR /Applications/freesurfer/7.3.2/mniSLE-PBS-h4tkn18vq6x3:~ timothydurazzo$ bedpostx_datacheck-bash: bedpostx_datacheck: command not foundSLE-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 E: laurenss@stanford.edu P: (650)-725-1716_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer