fMRIPrep on TBI data

[shilpitju]

Summary of what happened:

Hi,

I am trying to use fMRIPrep on TBI data. Can someone please suggest the strategy to be followed to circumvent the coregistration issues using Freesurfer due to the presence of lesions.

Thanks,

Shilpi Modi

[jsein]

Hi,

This section will interest you:

https://fmriprep.org/en/stable/workflows.html#cost-function-masking-during-spatial-normalization

[shilpitju]

Thanks so much. I ran two analysis, one with lesion and one without. The fMRIPrep output nowhere points to the lesion file, so I am not able to understand if lesion is taken care of or not. Attaching here the output files. It would be great if you can guide me in this.

With lesion

Without lesion

With lesion

Without lesion

With lesion

Without lesion

With lesion

Without lesion

With lesion

Without lesion

With lesion

Without lesion

With lesion

Without lesion

With lesion

Without lesion

With lesion