Mathias Goncalves

The goal of this PR is mirror workflow changes in fMRIPrep, splitting the processing into "fit" and "apply" modes. This is still a work-in-progress. New features: - `--level {minimal, resampling,...

`infant_recon_all` does not guarantee reproducibility

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### What happened? Looking through the `infant_recon_all` log, this line pops up a few times. ``` mris_sphere supposed to be reproducible but seed not set ``` ### What command did...

FEAT: Save CIFTI subcortical volumes

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Address #251 - My preference remains only outputting the CIFTI, and allowing users to derive this with `wb_command -cifti-separate COLUMN -volume-all ` - This will increase output size, as another...

FIX: Use tissue segmentations for FS recon-all

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The `recon-all` workflow uses the tissue segmentations, not an aseg, for brainmask refinement.

``` Node: nibabies_24_0_wf.single_subject_x_wf.func_preproc_task_rest_dir_PA_run_2_wf.bold_confounds_wf.concat Working directory: /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/concat Node inputs: acompcor = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/acompcor/acompcor.tsv aroma = cos_basis = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/tcompcor/pre_filter.tsv dvars = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/add_dvars_header/vol0000_unwarped_merged_dvars_nstd_motion.tsv fd = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/fdisp/fd_power_2012.txt motion = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/add_motion_headers/motion_params_motion.tsv rmsd = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/add_rmsd_header/sub-x_task-rest_dir-PA_run-2_bold_mcf.nii.gz_rel_motion.tsv signals =...

Currently, we are using the asymmetric dhcp cortical surface release, but a newer version of the template is available. We will likely need to apply a few steps to the...

ENH: Add MSMSulc

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Following implementation in nipreps/fmriprep#3085

### A short summary of what you would like to see in *NiBabies*. Some improvements that would go a long way: - Add/render workflow graphs (or mermaid graphs) - Add...

### Discussed in https://github.com/nipreps/nibabies/discussions/306 Originally posted by **Mak2055** August 10, 2023 Hello all, I have some skullstripped data that I would like to analyze using nibabies. When I flag "--skull-strip-t1w...

Add `auto` option to `--surface-recon-method`

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### A short summary of what you would like to see in *NiBabies*. This will decide on the best surface reconstruction, based on age. Roughly: | age | method |...