Oscar Esteban

FLAIR in BIDS input data not used for Freesurfer surface ``recon-all``

2

Reported with many details here: https://neurostars.org/t/fmriprep-flair-in-bids-input-data-not-used-for-freesurfer-surface-recon-all/2432/3?u=oesteban

Comes from #658, where @satra proposed: > - non-visual qa > [...] > - image similarity metrics (coregistration histogram separability), exposing bbregister mincost as a basic cut-off, distribution variance of...

Happened on TACC, after one of those results files errors (so it could also be that the merger node was required for this file to exist). ``` 191018-14:50:38,772 nipype.workflow ERROR:...

ds000051/sub-01 on TACC - file exists after execution. ``` Node: fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs_2_gii Working directory: /scratch/03763/oesteban/fmriprep-work/ds051-sub-01/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii Node inputs: annot_file = args = dataarray_num = environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects'} functional_file = in_file =...

CircleCI Optimization: skip costly nodes

3

The two main bottlenecks on the CI workflow causing a slow development iteration are: - Caching docker images (where there's little to do) - Long-running nodes (mainly based on ``antsRegistration``)....

Generate multiple surfaces

1

Convert this node in a mapnode that iterates over several depths. cc @satra for the actual values we need to iterate over https://github.com/poldracklab/smriprep/blob/a40cf9060960fcda2c3ecd21ab9add1f3bb8079d/smriprep/workflows/surfaces.py#L437

Suggestion: register interface std out and err with logging

3

Logging the outputs of interfaces has been a long-standing issue for Nipype 1.0 since its origins. Although I believe it currently solves the problem in a pretty acceptable way, I...

I think it is time to also brain extract BOLD with this amazing new tool.

Visualization of the ROIs in a probabilistic atlas

4

Probabilistic atlases (e.g., difumo) are not piecewise smooth. It would be interesting to weigh the colors of the ROIs and modify the alpha channel to make them transparent as you...

## Description The predict API of `SHOREFit` is not yet implemented. ## Way to reproduce Attempting to call `.predict()` on a fitted SHORE model will inevitably yield: ``` 88 if...