How to co-register the output of each pipeline to different spaces?

1

Hi,

I just downloaded the dHCP dataset. I’m still trying to understand the space in which each output volume and cortical surface are defined. After reading the paper by Sean Fitzgibbon et al., I assume that:

  1. The minimally preprocessed fMRI data is in native fMRI space.

  2. To map the fMRI data to the individual structural (T2w) space I should use the affine transform (subid_ses-id_from-bold_to-T2w_mode-image.mat)

  3. To map the fMRI to the neonatal volumetric template I should use the non-linear transformation (subid_sesid_from-bold_to-template40wk_mode-image.nii.gz)

  4. The individual cortical surfaces are natively defined in the individual T2w space. I need to follow the methods described in https://github.com/ecr05/dHCP_template_alignment to take it to the surface template space. Is that the same template available here by Bozek et al.?

Are these correct? Thank you in advance!

Diego

2

Hi Diego

Yes to all these qtns. Although you should note that (1) the space of the preprocessed fMRI is motion corrected native (not raw/scanner), and (4) a symmetric version of the surface atlas will be going up on the brain-development website any day now.

Cheers, Sean

3

Thanks Sean!

Best,
Diego