MAGeT for highres isotropic T2w and slab anisotropic scans

High resolution isotropic scans (0.64 mm^3) and slab anisotropic scans (2 x 0.4 x 0.4 mm^3) should be first preprocessed using the steps described in https://github.com/CoBrALab/documentation/wiki/T2-and-ADNI-slab-images-preprocessing .

T2w highres isotropic scans

The MAGeT folders must be initiated similarly as in standard MAGeT (https://github.com/CoBrALab/documentation/wiki/MAGeTBrain).

Only few minor changes need to be done in order to run MAGeT on highres isotropic T2w images

• Use the T2 extracted atlas brains found in /project/m/mchakrav/atlases_from_git/T2_extracted/ (do not take the *_flip.mnc) to populate the MAGeT folder input/atlases/brains/
• Rename these brains such as : mv brain1_t2.mnc brain1.mnc
• And then to run MAGeT, we used : mb run --stage-voting-procs 1 --stage-voting-walltime 24:00:00 , since the highres scans necessitate more time to run.
• And if it is still running out of time, the best approach would be to just try to rerun with the same command (mb run --stage-voting-procs 1 --stage-voting-walltime 24:00:00) without deleting any output files.

Slab anisotropic scans

This MAGeT run necessitate a bigger modification of MAGeT. Indeed, these scans have a small FOV focused on the hippocampus, and will therefore have difficulties to register the brains together. In order to facilitate the registration, we are therefore going to take advantage of the corresponding T1w images if available (which is the case in ADNI dataset for example).

This time, we will not be able to create automatically the structure of MAGeT directory. We will need to have the following directories instead

subject/brains/  where we will copy all the preprocessed T2w scans
subject/wholebrain/  where we will copy all the preprocessed T1w scans
template/brains/  where we will copy the 21 preprocessed T2w templates
template/wholebrain/  where we will copy the 21 preprocessed T1w templates
atlas/brains/ where we will copy the 5 T2 extracted brain atlases found in /project/m/mchakrav/atlases_from_git/T2_extracted/
atlas/wholebrain/  where we will copy the 5 T1w extracted brain atlases found in /project/m/mchakrav/atlases_from_git/T1_extracted/
atlas/labels/  where we will copy the 5 labels found in /project/m/mchakrav/atlases_from_git/hippocampus-whitematter/labels/

IMPORTANT : all our scans need to be named the same in subject/brains/ and subject/wholebrain for example.

To run MAGeT on this scans

git clone -b simplified-slab https://github.com/CobraLab/MAGeTbrain.git

mb run --stage-voting-procs 2 -j 2 --register_cmd mb_register_labelmask_antsReg_slab