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Hi Clément
The container `freesurfer/freesurfer:7.2.0` simply installs freesurfer into a docker container, and does not support use cases that require additional software.
There are a couple options. You could create your own container, which derives from `freesurfer/freesurfer:7.2.0` and install fsl there, or you could try to use my fork of neurodocker to generate a container, e.g:
``` docker run pwighton/neurodocker:latest generate docker \ --base-image ubuntu:xenial \ --pkg-manager apt \ --yes \ --fsl \ version=5.0.10 \ method=binaries \ --freesurfer \ method=binaries \ version=7.2.0 \ | docker build --no-cache -t pwighton/fs-tracula:7.2.0 - ```
But this has not been tested. If you try it out, keep me posted! I'm not sure if tracula has any other dependencies in addition to FSL. Maybe someone more familiar with tracula can chime in..
-Paul
On Thu, Mar 31, 2022 at 1:57 PM Clément Nicolas Graffard < clem.nicolas56@gmail.com> wrote:
External Email - Use CautionHi,
I am trying to use tracula within the freesurfer docker (freesurfer:7.2.0) but some commands related to fsl fail because the fsl script is not found.
For example, within the *trac-preproc* command, the subcommand* bet /input/inputData/sub-010017/dmri/lowb.nii.gz /input/inputData/sub-010017/dmri/lowb_brain.nii.gz -m -f 0.3 *is launched but this script is named bet.fsl instead of just bet in the folder */usr/local/freesurfer/bin *inside the docker. This causes the command to fail.
Have I missed some initialization steps ?
Many thanks,
Clément Nicolas--Graffard _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1GUq_z0pfTQYz4mpyEg5GHHW75caS4iBczyV9Atib4109lW... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1AKSNxFAF9zhrr5HyvxqYUt2gxSKpgp0jSiA8FLk78D16cL... < https://secure-web.cisco.com/1AKSNxFAF9zhrr5HyvxqYUt2gxSKpgp0jSiA8FLk78D16cL... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.