Add brainstem processing in ReconAll

[prioux]

It seems this has been put into a separate script. ReconAll produces this message when invoked with -brainstem-structures :

ERROR: the brainstem module is now a separate script: segmentBS.sh

For help, please execute the script with the flag --help: 

     segmentBS.sh --help

or visit the following page: 

https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures

[prioux]

The current container seems to be missing some matlab stuff too:

Singularity> segmentBS.sh --help

ERROR: cannot find Matlab 2014b runtime in location:

/usr/local/freesurfer/MCRv84

It is looking for either: 
  bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or
  bin/maci64/libmwlaunchermain.dylib (Mac 64b)

The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime.
You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2014b.
To do so, please run the following command (you might need root permissions):

fs_install_mcr R2014b

For further details, please visit https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime

[StongeEtienne]

Hi @prioux, Thanks for creating this issue.

On my computer I was able to install it by running (after FS install) : fs_install_mcr R2014b

and installing some missing package :

sudo apt-get install libncurses5
sudo apt-get install tcsh

[natacha-beck]

@prioux It is done, no ? Could we closed ?

[prioux]

Yes, the brainstem module is now supported in the FreesurfeReconAll 7.2.0 as integrated with the new integrator.

The initial commit was https://github.com/aces/cbrain-plugins-neuro/commit/a0c484abf3f2e742d780367fbf2da5619b87a66a

Since then, the amygdala segmentation module was also added in commit https://github.com/aces/cbrain-plugins-neuro/commit/dc3df255ddf564c5074be206372a68d29b21e2e3

I'm not planning to retrofit these modules in older versions of ReconAll.