Have you considered making a singularity/docker container with the required software?

[switt4]

I am trying to help a researcher set up the CBIG-0.10.2-Schaefer2018_LocalGlobal repository on a server running Ubuntu 18.04.3. I set up all of the paths for the required software libraries in a copy of the CBIG_gwMRF_tested_config.sh file. (The researcher is primarily interested in the Schaeffer2018_LocalGlobal stable project.)

After following all of the steps in the README.md, I sourced my .bashrc and was confronted with warnings that all of the versions of the required software that were already installed on the researcher's local server were the incorrect ones:

Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
FSL_DIR           /usr/local/fsl
[WARNING]: This version of CBIG repository's default FREESURFER version is 5.3.0.
You appear to be using FREESURFER 6.0.0 (which may or may not work with current repo). Switch to FREESURFER version 5.3.0 if possible.
Note: stable projects may not follow default setting, refer to the proper config file of the project you use. 

[WARNING]: This version of CBIG repository's default FSL version is 5.0.8.
You appear to be using FSL 6.0.1 (which may or may not work with current repo). Switch to FSL version 5.0.8 if possible.
Note: stable projects may not follow default setting, refer to the proper config file of the project you use. 

[WARNING]: This version of CBIG repository's default WORKBENCH version is 1.1.1.
You appear to be using WORKBENCH 1.3.2 (which may or may not work with current repo). Switch to WORKBENCH version 1.1.1 if possible.
Note: stable projects may not follow default setting, refer to the proper config file of the project you use. 

[WARNING]: This version of CBIG repository's default AFNI version is AFNI_2011_12_21_1014.
You appear to be using AFNI AFNI_19.1.18 'Caligula' (which may or may not work with current repo). Switch to AFNI version AFNI_2011_12_21_1014 if possible.
Note: stable projects may not follow default setting, refer to the proper config file of the project you use. 

ln: failed to create symbolic link '/usr/local/CBIG-0.10.2-Schaefer2018_LocalGlobal/.git/hooks/pre-commit': No such file or directory
ln: failed to create symbolic link '/usr/local/CBIG-0.10.2-Schaefer2018_LocalGlobal/.git/hooks/pre-push': No such file or directory

Nowhere previously in any of the documentation do you specify which versions of these dependent softwares are required.

Given that your tool has such specific requirements, have you considered making a singularity and/or docker container with the correct versions? Or can I just safely ignore these warnings and continue with the newer versions of the dependent softwares?

Thanks,
suzanne

[rubykong]

@switt4 The Schaefer parcellation does not depend on these softwares, it mainly contains matlab scripts. So you can ignore these warnings if you are only interested in the Schaefer2018_LocalGlobal project. You received these warnings is because some other projects in our lab might be affected by different versions of these softwares.
We did consider making a docker container, but we haven't seen any one suitable for matlab scripts. Would appreciate if you have some suggestions!

[rubykong]

@switt4 BTW, you can always try to run the example we provide in Schaefer project to see if you can replicate results as the example results: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/examples