Within-subject alignment across 3 sessions

AFNI Message Board
1

I’m currently working on a longitudinal analysis of fMRI data across three timepoints and am trying to puzzle out how to do within-subject alignment of the three structural images (and their corresponding functional images) in an unbiased fashion- i.e., not just align timepoints 2 and 3 with timepoint 1 but align all three timepoints to a more ‘neutral’ position so that all three datasets are being manipulated to a similar extent. In the past, I’ve followed Daniel Glen’s recommendations for how to do this across two timepoints (https://sscc.nimh.nih.gov/sscc/dglen/alignmentacross2sessions) but it’s not obvious to me how to scale this up for three (or more) timepoints without biasing toward one of the timepoints.

In a pinch, I know that I could just transform each timepoint into standard space separately, but we are planning on doing our analyses in native space and as these participants are older stroke patients, transformation to a template is not always straightforward (or desirable), so I’d like to avoid that if possible.

Any thoughts or suggestions from the AFNI experts?

Thanks!

  • Kate
2

You could just use the same in-between S1 and S2 time point, or you could add on to that to calculate a new in-between S2-S3 anatomical. Then compute the in-between of the in-betweens. There is no existing script for this, but it could be fairly easy to extend the two-session script to that. If you have many sessions, then you could generate a new template for that using the @_to_MNI_Qwarpar script. A lot of this depends on how far you want to go in terms of complexity. Most just use an initial session and settle on that.

3

Daniel’s suggestion is probably easier and likely about the same end result. I might suggest you use Freesurfer[/url] to build an unbiased anatomical template using their [url=https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing]Longitudinal pipeline. Then using their version of an unbiased brain, I would run @SUMA_Make_Spec_FS to generate a NIFTI version of brain.mgz (now brain.nii) and use that as your skull-stripped anatomical for future processing in AFNI.

Happy to try and break this down further!