Oscar Esteban

SDC - Horrible co-registration of *b=0* reference and EPI reference

1

The inputs to `antsRegistration` when finding the misalignment between the fieldmap reference and the target DWI (via its *b=0* reference) is currently unacceptable for our dataset ds001771. This problem is...

Comes from https://github.com/nipreps/dmriprep/pull/144#discussion_r561782596

Framewise displacement calculation

1

Based on the estimation of #94, extract some score of the relative rigid-body misalignment of each orientation. We will identify volumes that are outliers in terms of head motion, or...

Determine number of shells

1

I know @edickie and @mattcieslak were working on this. I would suggest adding this as a cached method (i.e., only called once and then cached) of the ``DiffusionGradientTable`` object https://github.com/nipreps/dmriprep/blob/0a609b4c91c97b6b2bb0fad0f35ce2e7d15f44b3/dmriprep/utils/vectors.py#L12-L178

Integrate SynthStrip?

8

Considering the incredible success with MRIQC (@ahoopes SynthStrip is amazing), I think we could consider the integration of SynthStrip here.

Check continuity of fast-track, esp. multi-session datasets and w/cohort normalization

8

#219 and #223 will likely break some parts of the anatomical fast track. Let's make sure it works before cutting 0.7.

MP2RAGE skull-stripping

14

Make MP2RAGE amenable to `antsBrainExtraction.sh`. One possibility, as @chrisfilo mentioned in #231 is using the inversion echoes https://github.com/poldracklab/pydeface/pull/15.

Calculate Euler numbers and place them in the sidecar json of surfaces.

8

This issue entails: - Sending a PR to nipype with an interface for `mris_euler_number` (we could have it first in niworkflows if that eases the process). - Adding a node...

Fast-track not finding all expectations with ``--cifti-output``

3

I believe the problem comes from the "hidden" MNI152NLin6Asym space.

From #6: - [ ] Transform files will need extensive metadata