fMRIPrep: preprocessed data in native BOLD space

fmriprep
#1

I have a special case where I do need to do analysis in native space - I’ve implemented Henning Voss’ hypersampling method (https://arxiv.org/abs/1804.10650) to produce cardiac pulsatility maps, and that requires you to work on the raw BOLD data before motion or slice time correction (since you use the temporal oversampling provided by the slice acquisition rate, and you need to know which acquisition slice each voxel is in). So I end up with maps in native BOLD space that I’d like to get to T1 or MNI space to overlay on the anatomy and match up with other maps (which I can do in T1 or MNI space). I don’t mind if I have to fish the transforms out of the work directory (although I’d prefer that they be in the appropriate func directory), but I can’t find them anywhere - are they ever saved?

Fmriprep error processed in native bold space error in "native" space (--output-spaces func)
FMRIPREP: spatial normalization
#2

For clarity - would you mind posting this question as a new topic?

#3

Sure thing - wasn’t sure if I should do that.

1 Like
#4

Hi @bbfrederick, this is now possible after version 1.4.0.

#5

Great! How do I enable this? I’ve tried adding the “run” and “func” output spaces (they seem to be synonyms), and I get preprocessed data in native space (yay!), but the BOLD to/from T1w (or BOLD to/from MNI) transform files don’t seem to be present.

(Edited for clarity)

#6

Correct

Correct, can you open an issue to request this feature in our repo?

EDIT: There is an issue open already - https://github.com/poldracklab/fmriprep/issues/1184