NIFTI connectivity outputs for DK atlas

1

Hi there,

I would like to generate XCP-D timeseries and the functional connectivity matrix results for the DK atlas since I also have DWI structural connectivity results available for such atlas regions.

Checking XCP-D connectivity code, I was wondering if using the NiftiConnect() interface (or a similar workflow) would work.
In my specific case however I would use BOLD mask (*_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz), atlas labels (desc-aparcaseg_dseg.tsv) and atlas segmentation (*_task-rest_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz) files available via fMRIPrep as FreeSurfer segmentation/parcellation results resampled into BOLD grid at MNI standard space.

Am I missing something else?

Many thanks,
Jordi

2

Hi @jhuguetn,

This part of the documentation seems relevant to you. You would want to run run XCP_D after making your custom atlas (e.g., using Nilearn). It is not recommended to try to run the individual nodes that make up the XCP_D pipeline outside of the formal workflow.

Best,
Steven

3

Thanks @Steven.
Documentation suggests to use Nilearn’s NiftiLabelsMasker for my specific use-case (ie. default NIFTI pipeline, no cifti option). That’s basically what the XCP-D NiftiConnect interface code seems to do but additionally dealing with parcels coverage. Right?

I could write a custom script following a similar approach but using my own (FreeSurfer DK-based) parcellations. Would that be ok?