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installation
The softwares required and their installation process is mentioned below:
FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.
wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz
The url may change according to the version. There is currently no distribution for ubuntu 20 but we can use the distribution for ubuntu18.
tar -zxpf freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz
Once unzipped, an additional freesurfer folder will be created. Post that we need to set up freesurfer executable path. Usually this steps need to be done everytime a terminal session is created. But we can add it into .bashrc to automate the process. In either case, either add this line into .bashrc or run it when you open a terminal
export FREESURFER_HOME=<path to freesurfer>/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
Verify $FREESURFER_HOME points to the correct path.
Go to here and register your details.
Post registration a license.txt would be sent to the given mail address, store it in the folder mentioned in $FREESURFER_HOME.
This can be found by echo $FREESURFER_HOME.
We can check if freesurfer has been properly configured and running by using which freesurfer and which freeview.
If your academic institution gives matlab full version download the zipped file for your respective OS.
Then unzip the file.
Open terminal and go the the unzipped matlab folder. Then initiate install file.
./install
Follow the steps in the gui and install matlab.
There are different ways of starting matlab.
First, while installing matlab we are given an option to create symlink , if you selected this option and was successful in installing and creating the link,
we can start matlab by simply typing matlab in the terminal.
Second, in case the symlink was not successful and/or we didnot select that option, then we can run matlab by ./<path to matlab folder>/bin/matlab.
Third, we can create a symlink by following command
sudo ln -s <path to matlab installed folder>/bin/matlab <path to simlink folder>/<symlink name>
Post generating symlink we can open a terminal and type symlink name to start matlab.
It is a package for analysis of brain imaging data .
The zipped file can be downloaded :
wget https://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip
wget http://www.fil.ion.ucl.ac.uk/spm/download/spm12_updates/spm12_updates_rxxxx.zip
The updates version needs to be placed in place of _rxxxx.zip.
Open the terminal and go to the path where the spm12.zip has been downloaded.
unzip spm12.zip
unzip -o spm12_updates_rxxxx.zip -d spm12
Open matlab, on Environment tab of the workspace , click on Set Path , then click on Add Folder and then go to the spm12 folder and save this folder. This will add the spm12 folder into the matlab path for execution.
cd <path to spm12 folder>/src
make distclean
make && make install
make external-distclean
make external && make external-install
Troubleshooting
- mex : Command not found
Create symlink to mex in matlab folder.
sudo ln -s <path to matlab folder>/bin/mex <path to symlink folder>/mex
Then close and restart terminal and continue the compilation.
Full installation step and further troubleshooting can be found here.
MeshLab is an open source, portable, and extendible system for the processing and editing of unstructured 3D triangular meshes.
Update the apt-get command line tool. This is done to ensure that all linux packages and their metadata are updated.
sudo apt-get update -y
Install meshlab in ubuntu.
sudo apt-get install -y meshlab
Run the following command from the terminal (location does not matter). If it has been installed properly, meshlab gui would start.
meshlab