Freesurfer
Last modified by Xwiki VePa on 2024/12/10 12:41
Freesurfer 6.0 is available by default in VDI Cubbli installations and pultti-18.it.helsinki.fi. If you need it on local installation, you can install it with sudo apt install cubbli-freesurfer. For documentation see Freesurfer home page https://surfer.nmr.mgh.harvard.edu/
Before you use Freesurfer you need to set up its environment with SetUpFreeSurfer.sh script:
jjaakkol@vdi-cubic-005:~$ . /opt/freesurfer/SetUpFreeSurfer.sh Using Cubbli default FREESURFER_HOME=/opt/freesurfer-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /opt/freesurferFSFAST_HOME /opt/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /opt/freesurfer/subjectsMNI_DIR /opt/freesurfer/mnijjaakkol@vdi-cubic-005:~$
If the directory /opt/freesurfer/ is missing Freesurfer isn't installed in that host. Install it with apt (see above) or ask helpdesk for help.
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