External Email - Use Caution
On linux, that file is under $FREESURFER_HOME/bin and will be found in your PATH after you setup the Freesurfer environment, e.g. for the 7.2.0 release installed via the .rpm file, you setup the environment with, $ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0-1 $ 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/7.2.0-1 FSFAST_HOME /usr/local/freesurfer/7.2.0-1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.2.0-1/subjects MNI_DIR /usr/local/freesurfer/7.2.0-1/mni $ which segmentBS.sh /usr/local/freesurfer/7.2.0-1/bin/segmentBS.sh $ segmentBS.sh -h ERROR: cannot find Matlab 2014b runtime in location: /usr/local/freesurfer/7.2.0-1/MCRv84… rest of output deleted .. So if you have not already installed the MATLAB runtime environment for the segmentBS.sh script, then you need to run the Matlab install script we provide. For the Freesurfer install under /usr/local on linux, the Matlab install needs to be done with root/admin privileges which you can try via the sudo option, $ cd $FREESURFER_HOME/bin$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2014b … you will see output from downloading and installing the matlab runtime under /usr/local/freesurfer/7.2.0-1/MCRv84 …You should follow the instructions from the script output about how to set LD_LIBRARY_PATH, e.g., On the target computer, append the following to your LD_LIBRARY_PATH environment variable: /tmp/tmp.e23XcWLTeV/install-target/v84/runtime/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/bin/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/sys/os/glnxa64: Your paths may be different, but you would modify the LD_LIBRARY_PATH setting as follows; I just cut and pasted the /tmp/* paths anover after "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:”, $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/tmp/tmp.e23XcWLTeV/install-target/v84/runtime/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/bin/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/sys/os/glnxa64 You could follow the same instructions as listed above for the 7.4.0 release, i.e.. change 7.2.0 to 7.4.0 in all the commands (and corresponding output should list 7.4.0 instead). The segmentBS.sh in 7.4.0 might ask for a newer Matlab version like MCRv97. In that case, the sudo command to run the fs_install_mcr script would be,$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b Once Matlab runtime is installed, try running segmentBS.sh again, $ segmentBS.sh -h Directory of subject to process: /usr/local/freesurfer/7.2.0-1/subjects/-h does not exist So change SUBJECTS_DIR to the path containing the subject data you want to process, $ export SUBJECTS_DIR=/path/to/my/subjects … then try running again ...
- R.
On Dec 26, 2023, at 19:32, Ganjizadeh, Ali, M.D. <Ganjizadeh.Ali@mayo.edu> wrote:segmentBS.sh