MRIQC custom brain template

Software Support
1

I want to use MRIQC to extract metrics for ultra-low-field, infant MRIs. Because of the differences in brain shape and in image contrast, I would like to use our own (age-specific) templates, and I have a couple of questions:

  1. What files are required to be included with the template? Feeding the mriqc repo into an AI tool (Claude), it reports that it only needs:
  • res-02_desc-brain_mask — normalization reference mask
  • res-01_label-CSF_probseg, res-01_label-GM_probseg, res-01_label-WM_probseg — probability masks
  • res-02_desc-fMRIPrep_boldref
  • res-01_desc-carpet_dseg

Is this accurate?

  1. If only those files are actually needed, would it be OK to remove the other hundred files included in the nipreps/mriqc Docker image, under “/templateflow/tpl-MNI152NLin2009cAsym” to reduce the size of the image?
2

Is this accurate?

Sounds about right

If only those files are actually needed, would it be OK to remove the other hundred files included in the nipreps/mriqc Docker image, under “/templateflow/tpl-MNI152NLin2009cAsym” to reduce the size of the image?

Yes, absolutely. Please send a PR removing anything that’s not needed!

Regarding your initial question on how to feed custom templates, please check Python Client - TemplateFlow . Adding your custom template to templateflow would then allow MRIQC to select it for processing.

We’d be very interested in adding your new features to MRIQC, should you send a PR!