Céline Provins

ENH : separate deep from shallow WM+CSF in the carpetplot

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This PR implements the proposition of @effigies (https://github.com/nipreps/niworkflows/pull/651#issuecomment-961103549) to separate the WM+CSF compartement in the carpetplot into the shallow WM+CSF and the deep WM+CSF corresponding to the aCompCor mask

fMRIprep try to access layout_config file in .git folder

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### What happened? I wanted to run fMRIPrep via docker on a dataset installed locally and handled by datalad. However, the run fails, because fMRIprep tries to access `/data/.git/refs/objects/layout_config.json` but...

Rating widget : modify selectable list of artifacts

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Based on my observations in the bad quality dataset, I would like to propose some modifications of the list of artifacts that can be selected. - Add a signal drop-out...

[The MRIQC documentation](https://mriqc.readthedocs.io/en/stable/docker.html) should point to the latest version of the `docs/source/docker.rst`, because in the current version the MRIQC docker is still listed under poldracklab.

Binder doesn't set up the right environment

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Hi, I wanted to complete the notebooks interactively using Binder. However, nipype don't seem to be installed in the environment as the module is not found when it should be...

### What would you like to see added in fMRIPrep? Following the migration of the report generation to nireports (#3177), the count of the number of crash files under the...

### What happened? The workflow still runs successfully until the end, but this error is reported. ### What command did you use? ```shell DATADIR="/oak/stanford/groups/russpold/inprocess/cprovins/hcph-dataset/" DERIVATIVEDIR="/oak/stanford/groups/russpold/inprocess/cprovins/hcph-derivatives" CODEDIR="/oak/stanford/groups/russpold/inprocess/cprovins/code" SUB="sub-001" STUDY=`basename $DATADIR` IMG="/oak/stanford/groups/russpold/users/cprovins/singularity_images/fmriprep-23.2.0a2.simg"...

Report clearly bids filters

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### What would you like to see added in fMRIPrep? It would be nice that the bids filters were reported very clearly in the log file (and perhaps make them...

FIX: copy name attribute of dataset_description.json from input dataset

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Currently, the name attribute in "dataset_description.json" in the MRIQC derivatives is always set to "MRIQC - MRI Quality Control" I propose instead copying the name from the input dataset.

Compute only one set of IQMs and files for multi-echo dataset

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In its current behavior, MRIQC generates one set of timeseries (`timeseries.tsv`) and one set of IQMs (`bold.json`) per echo in a multi-echo dataset. This behavior is illogical because the multiple...