Make MNI space projection and ROI based analysis default for ANTs: Ofer

[tashrifbillah]

The request has not been agreed upon.

2. When running —StudyTemplate, currently the output will be in the original space coordinates (e.g., if 2X2X2, the output would be registered 2X2X2, and 2X2X2 skeleton). A better option would be that the output is in MNI space. I think that this can be achieved by setting the -template flag? (e.g, setting it to the FA image provided by FSL, or the one provided by ENIGMA?)

Correction: This is achieved by --space flag.

but I think registration to MNI should be the default option when using the StudyTemplate option. ... I think it would be better if an option could be set to NOT register to MNI (which will be evoked when using animal data for example).

I have reviewed my work flow. An "if" condition after this line can do the job. Shall I do it?

args.space=` pjoin(fslDataDir, 'standard', 'FMRIB58_FA_1mm.nii.gz')

Please double check the above template defines MNI space you referred to.

The code should also generate the ROI values for the regions in the MNI space by default.

Are we sure we want to do this? Because it will take time to do ROI based analysis. Again, it can be done with an if condition setting:

args.lut = pjoin(enigmaDir, 'ENIGMA_look_up_table.txt')
args.labelMap = pjoin(fslDataDir, 'atlases', 'JHU', 'JHU-ICBM-labels-1mm.nii.gz')

Again, do we want ROI based analysis based on using the the above LUT and ATLAS?