Preprocessing with SBRef image in AFNI

AFNI Message Board
1

Hello,

I’ve got SBRef image with new scanning protocol, so I can use this SBRef image for motion correction and for alignment of BOLD images to anatomical images.

Our experiment consists of 7 runs and for each run there is one SBRef image file with the file name extension IMA.

Previously, I used the nearest BOLD image to anatomical scan for motion correction and alignment of other BOLD images to anatomical images.

Can you explain how I can use this SBRef image for the preprocessing?

I think I should transform this IMA file to the specific form first and then apply it to the preprocessing, but don’t know much about it.

I’d be appreciated to your help. Thanks.

2

If you used a single SBRef (just one, for all 7 runs),
then it could be passed to afni_proc.py via the option
-volreg_base_dset, and it would be used for both
anatomical and EPI registration.

But there is no mechanism to use 1 per run.

Having 1 per run suggest to me that perhaps the scanner
is doing a shim each run. If that is indeed the case,
the registration steps should be done per run, not
across all 7 at once. In that way, the EPI → anat
registration drives cross run alignment, rather than
EPI → EPI.

But this also has the trouble of introducing distortion
patterns across the runs, any time a re-shim is done.

To me, the important question is whether the shimming
operation was performed in each run.

  • rick
3

Dear Rick,

For multi-band sequence, will you recommend using -volreg_align_to MIN_OUTLIER or to align to the Single Band reference image taken at the start of the scan? (Sbref)

4

It depends on how the SBref looks in relation to the typical EPI. Of course, you also have to worry that the subject might have moved during the SBref acquisition. Let's assume not, though of course it is a concern.

If the contrast of the SBref image looks very much like the other EPI, then it could be used. If it looks a bit different, it might be "noisy" to align each EPI volume to it.

One other option would be to align the EPI to the global MIN_OUTLIER, but then have SBref used for anatomical alignment (along with MIN_OUTLIER->SBref). For this, consider:

-align_epi_ext_dset SBref
-volreg_align_to MIN_OUTLIER
-volreg_align_e2a

Alternatively, you could align each run to its local MIN_OUTLIER volume, but then align all of those to the SBref, which would be used to align with the anat. That is at least fewer alignments to the SBref.

-volreg_base_dset SBref
-volreg_post_vr_allin yes
-volreg_pvra_base_index MIN_OUTLIER

I would be inclined to go the -align_epi_ext_dset route here.

  • rick