Patrick Sadil

Sharp edge near posterior of some brain masks

6

With the current version of MRIQC (22.0.1), some proportion of participants end up with brain masks that have a sharp boundary that excludes part of the occipital pole.  I...

Looking at the inputs and outputs for a run that included the `--correct-slice-timing` flag, and it seems like no correction is being applied (e.g., the voxel that had the largest...

[ENH] Improve plotting contours for `PlotlySurfaceFigure` objects by adding `add_contours` method

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- Closes #3711 Changes proposed in this pull request: - Add `add_contours` method to `PlotlySurfaceFigure`, increasing customizability of contour lines. - Added example of the method in [plot_3d_map_to_surface_projection](examples/01_plotting/plot_3d_map_to_surface_projection.py)

`result_xfm` in `Dataset.status()` seems broken

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### What is the problem? There seems to be a documentation issue or a bug in `Dataset.status()`. The api has a `result_xfm` option `"metadata"`, but using that in a typical...

`datalad save` slows down superlinearly with larger numbers of files (but not git annex add)

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### What is the problem? I'm working with rather large datasets (10k - 100K files) and `datalad save` is taking much longer than seems necessary. For example, in one dataset,...

### What happened? It looks like the IQMs are not submitted to MRIQC's metrics repository when the `--fft-spikes-detector` is turned on, and that this is due to a mismatched schema....

### Summary While I was working on a pull request, [typos were found by `codespell`](https://github.com/nipy/heudiconv/pull/614#issuecomment-1462677835). I see that there is [a github action for running `codespell` on all pull requests...

omp_nthreads not passed to merge_and_denoise_wf on one branch

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## Summary The merge_and_denoise_wf has a few nodes that can benefit from multithreading, but it looks like there is one instance where omp_nthreads isn't passed. https://github.com/PennLINC/qsiprep/blob/89ba85b3cbdba4c0afad875c29d63154c6aa1fc7/qsiprep/workflows/dwi/pre_hmc.py#L320-L335 This results in a...

Allow `topup` to use multiple threads

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## Summary `topup` can be started with multiple threads ```shell ❯ topup --help 2>&1| grep threads --nthr Number of threads to use (cannot be greater than numbers of hardware cores),...

### Your idea This is to continue a conversation that started on Neurostars: https://neurostars.org/t/are-there-recommended-ways-of-storing-dtype-information-alongside-bids-tabular-files/29601. I'm working with a fairly large dataset (thousands of participants, many of which have multiple sessions),...