Matt Cieslak

The high values of FA are from poor model fits, I believe. I don't have a recon spec that creates a colorFA file. If you're looking to do DTI-centric analysis,...

hi @sebnaze could you post your singularity command?

Hi @Giuseppe1988, you've found a bug or at least something that's not well documented. Does your data have multiple T1w images per subject? Those "mode" transforms are supposed to be...

To add a new atlas you'll need to make sure its aligned with [this image](https://github.com/PennLINC/qsiprep/blob/master/qsiprep/data/mni_1mm_t1w_lps.nii.gz) in world coordinates. I recommend using ITK SNAP to check because it interprets headers the...

This suggests that you didn't collect two of the exact same dwi schemes in different phase encoding directions. If that's the case you should remove `--distortion-group-merge average`.

This mirrors the behavior of fMRIPrep, where a single anatomical scan is created for each subject.

Hi! I'm not sure what may be happening here, but for reference here is a recent command I ran for the sifthsvs command that was successful: ``` singularity run \...

ahhhh 🤦 you've uncovered a bug. When someone runs `--dwi-only`, qsiprep is supposed to grab the skull stripped t1w from freesurfer and use it in the anatomical workflow. The non-`--dwi-only`...

If you only have PhaseEncodingAxis, you should check with the person who acquired the scans as to which scan contained which phase encoding direction. Supposing the PhaseEncodingAxis is `j`, you...

Hi! Can you confirm that both images have the same exact set of bvals and bvecs?