Daniel Lurie

Provide a lattice view of multiple carpet plots as part of the group level outputs.

2

I've found this a really useful way to get a sense of the data visually, and how the noise levels/patterns in one scan relate to other scans. I'll likely try...

ICA component images do not load in functional report

9

MRIQC v. 0.9.2 (not running via Docker/Singularity, unfortunately). Running with `--ica` produces a `melodic_reportlet.svg` image in the working directory...  ...but the ICA plots don't load at all in the...

Enhancement: Include subject ID in crash filenames.

1

This would be very useful when running on large datasets, where it's fairly easy to end up with dozens or hundreds of crash files. Figuring out the set of subjects...

How to handle lesion masks, including multi-session data?

2

This question came up in the context of how `smriprep` should handle multi-session data that has associated lesion masks (see https://github.com/poldracklab/smriprep/issues/58), but I think it raises a BIDS question too....

# Bug Report **Specifications:** - App Version: 4.4.0 - OS (macOS, Windows, Linux): Mac OS 11.6.4 **Description:** Links open in Chromeless app instead of default browser (Google Chrome). **Steps to...

Also included is the alternative band-aid script I originally wrote while troubleshooting.

Exclude lesioned areas from confound masks.

20

Segmentation algorithms are often confused by lesioned areas, resulting in incorrect automated segmentation results in these regions. As such, it is good practice is to subtract the lesion mask from...

- `plot_carpet` now lives in a dedicated `plotting.py` file - The main `denoise` function has been moved to `denoiser.py` for ease of importing - `run_denoise.py` has been streamlined. - Fixed...

Question: Why is d = k + 1 for Kaiser and Broken Stick?

1

I noticed that the ID estimates provided by the `Kaiser` and `broken_stick` methods in `id.lPCA` are `k + 1`, where `k` is the number of components to be kept according...