Install Request: FreeSurfer 7.2 [IN05077530]

[balston]

User needs access to additional functionality available with FreeSurfer 7.x.

FreeSurfer site here: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki

See:

266 and #367

for previous install details.

[balston]

FreeSurfer 7.x installation guide and downloads available from here:

https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads

We will need to download the _freesurfer-linux-centos8_x8664-7.2.0.tar.gz archive file.

[balston]

As usual the FreeSurfer download is very slow (~1 hour on Myriad) so I'm downloading to my laptop and will then upload it into /shared/ucl/apps/pkg-store/ on Myriad and the build script will pick it up from here.

[balston]

_freesurfer-linux-centos7_x8664-7.2.0.tar.gz has now been uploaded to /shared/ucl/apps/pkg-store/ on Myriad. Next step is to copy the version 6 build script and update it to work with this version.

[balston]

I'm trying to work out if we need to install a new license file for this version.

[balston]

OK looks like I need to complete the following form to get a new license key file:

https://surfer.nmr.mgh.harvard.edu/registration.html

[balston]

I've completed and submitted the license request form.

[balston]

FreeSurfer license has been emailed to me. I've uploaded it to:

/home/ccspapp/Software/freesurfer/license-7.2.txt

It is only readable by the ccspapp account.

[balston]

I'm now updating the build script.

[balston]

Updated. Running as ccspapp:

cd /shared/ucl/apps/build_scripts
./freesurfer-7.2.0_install

[balston]

Module file ready for testing and test job submitted.

[balston]

My test job keeps erroring so I need to do some more investigation.

[balston]

Found what I'm looking for to help get the test example running correctly:

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

[balston]

I've now updated submitted my test job using the suggestions in the testing documentation.

[balston]

I think this time the job has started running successfully. It's going to take a few hours to complete if it works.

[balston]

I've now managed to check the output from the test job which was running:

recon-all -openmp $NSLOTS -s bert -all

on the Bert test subject. It appears to have worked. Next step is to add a module file for this version.

[balston]

Module file now on Myriad.

Need to load the following modules to use FreeSurfer 7.2.0:

module load xorg-utils/X11R7.7
module load freesurfer/7.2.0

[balston]

User informed.

Done on Myriad.

[balston]

Now also done on Kathleen.

Shouldn't install on the Tier 2 clusters.

[balston]

User has confirmed it is working. Closing.