Hi, I have a question regarding the dMRI data in the PROCESSED folder. 

I believe the data in the PROCESSED folder is an additional step from AutoQC. Specifically, I think it is a version of AutoQC data that has isotropic voxels. You can see this on the .nii and/or .nrrd metadata. Voxel dimensions in AutoQC are ~0.65 × ~0.65 × ~1.30 mm while in PROCESSED are ~0.65 × ~0.65 × ~0.65 mm.

The main reason we are interested in using the data in the PROCESSED folder is not because of the resolution, but because it already contains a brain mask (brain segmentation). Having this mask means we don't have to deal with fibers originating in surrounding (non-brain) tissues. That would also help for future co-registration to the structural MRIs.

Unfortunately, the DTI data (tensor data) in the PROCESSED folder seems to have problems. The tractography reconstruction generated in Diffusion Toolkit makes no sense: all fibers have the same orientation (see image attached). I initially thought this was a problem on my side (that I had used wrong parameters), but others get similar results. 

So did the data in PROCESSED not undergo tensor reorientation during resampling and is actually not intended for analysis? Can the data in PROCESSED can be used for analysis and tractography reconstruction? Or are brain masks available for data in AutoQC?