Get everything working on Quartz

[SammyRigdon]

Due to an unexpected outage of BigRed200 all scripts need to be double checked for working on Quartz so we can continue working. Additionally, where possible, references to sepecific systems shouldn't be used to minimize changes between scripts, for example instead of /N/u/{user}/Quartz we should use ${HOME} instead so that i t works on both systems.

• [x] Installation Scripts
  • [x] MSM
  • [x] Ciftify
  • [x] Workbench
• [x] Utility
  • [x] Ciftify_Subjetc_List
  • [x] ADNIPostProcessing
• [x] CurvatureCorticalSA
  • [x] ADNI_Curvature_CorticalSA
• [x] RunMSM
• [x] RunCiftify

[SammyRigdon]

@garciake mentioning you for progress tracking

[SammyRigdon]

On commit 7acc9c9 we needed to remove the copying of freesurfer and fsl from installation scripts as quartz has a much smaller disk quota limit than bigred200. Will continue testing to ensure things still work correctly

[SammyRigdon]

After removal of copying files and pointing towards the file locations in slate Ciftify is now working on Quartz. Bear in mind we may need to occasionally update the script if the software library changes file structure

[SammyRigdon]

Workbench install worked perfectly with no edits necessary. All installation is working as expected. Moving on to utility and data scripts

[SammyRigdon]

Subject list generation works as expected

[SammyRigdon]

New Slurm allocations need to be made for quartz so that we can run Ciftify and MSM.

[SammyRigdon]

Everything appears to have worked correctly on quartz for Ciftify and MSM

[SammyRigdon]

Datasheet generation working. Will test post processing images next

[SammyRigdon]

All post processing worked on quartz closing issue