Install Request: FreeSurfer 7.4

[heatherkellyucl]

IN:06092300

Wanted for EasyReg "deep learning registration of brain MRI", which exists in 7.4: https://surfer.nmr.mgh.harvard.edu/fswiki/EasyReg

Uses tensorflow? Checking to see which version it would want to install as the docs do not say.

Paper A ready-to-use machine learning tool for symmetric multi-modality registration of brain MRI says "The networks are implemented in TensorFlow/Keras. Crucially, the inference code is implemented in a version of Python that is distributed with FreeSurfer, such that users do not need to create virtual environments and install dependencies."

[balston]

Build script:

freesurfer-7.4.1_install

ready to test on Myriad.

[balston]

build script is erroring at the MATLAB runtime stage:

ERROR: must set FREESURFER_HOME before installing
INFO: if you're using sudo, make sure to pass the FS home variable with
INFO: sudo FREESURFER_HOME=$FREESURFER_HOME fs_install_mcr R2019b

We didn't need this with the previous version. Will correct and rerun.

[balston]

I think it needs to be:

export FREESURFER_HOME=${INSTALL_PREFIX}/freesurfer

trying this in the build script.

[balston]

This time the build script completes with out errors.

[balston]

module file ready.

Now need to test.

[balston]

Almost there - I forgot to download and install an updated license file.

[balston]

With an updated license file my test job looks more promising - it's been running for 20 mins now.

[balston]

Test job worked! Took almost 3 hours to run.

[balston]

User contacted.

[heatherkellyucl]

(Does this still need installing anywhere else or is it done?)

[balston]

FreeSurfer doesn't support MPI so we don't really need to install it on Kathleen.