Preprocessing for atlas based connectivity matrices

[effigies]

@michael

I still got the same error though, and had to add --reg dummy.dat for your command to work, was that the right thing to do?

I think you actually need to add --regheader to mri_vol2vol as well. Sorry for not catching that, earlier. If that works, let me know, and I’ll update the command above.

@michael

An important question: I thought fmriprep/sub-<subject_label>/func/sub-<subject_label>_task-rest_bold_space-T1w_preproc.nii.gz was in the same space as the T1, but they have different voxel size (~ 3mm isotropic for the first, and ~ 1mm for the latter)

When we say the BOLD and T1w images are in the same space, what we mean is that they have been coregistered such that the same RAS coordinates in either get you the same brain structure. It is very rare that someone would want to upsample their BOLD data into T1w resolution, I think.

@michael

Does the fmriprep pipeline align the bold data with the T1 data (…T1w_preproc.nii.gz being the result) but without resampling to T1 space?

Exactly.

@michael

To compute the connectivity matrices, I would need the bold data exactly in the same space as the aparc+aseg in native T1 space (that includes same voxel size). Would you have any suggestion on how to do that? (Having aparc+aseg with the same low resolution as the bold data would be fine and maybe preferable to avoid further processing of the time series)

Ah, yes. You’ll still need to down-sample. You can probably do this directly by switching from using T1w_preproc.nii.gz to one of your BOLD outputs, in both the tkregister2 and mri_vol2vol commands, but you should really verify this…