AFQ now supports normalization with ANTs

[Jason Yeatman]

Dear AFQ users,

I have recently updated AFQ to include an option to use ANTs for normalization rather than SPM. Generally I have been very happy with the accuracy of ANTs for alignment so I am beginning to rely more on their tools. But I'm also interested in your feedback/suggestions.

Once ANTs is installed on your system you can define what software is used for normalization when you create the afq structure (spm is the default). For example:

afq = AFQ_Create('sub_dirs', sub_dirs, 'sub_group', sub_group, 'normalization', 'ants');

From this point everything should run smoothly. If you notice anywhere for improvement (or catch a bug) let me know.

Jason

[Loxlan Kasa]

Great tool Jason and the AFQ team. A quick question, am trying to  transform the MNI ROIs

to native space using the antsInvWarps, what output file form ANTs should I use as the input to the  AFQ_SegmentFiberGroups? I have 0GenericAffine.mat, 1InverseWarp.nii.gz, 1Warp.nii.gz and the Warped.nii.gz. Should I name the files in a special way and just provide the path to AFQ_SegmentFiberGroups so the needed ANTs output will be automatically identified?  Thanks inadvance.