How to transform the ROIs drawn before to fit the new functional datesets?

AFNI Message Board
1

Hi,
My anat (1mmX1mmX1mm each voxel) and EPI datasets (1.5mmX1.5mmX1.5mm) were preprocessed using uber_subject.py before with the steps of auto block,despike,align,tlrc,volreg,blur,mask,scale and regress.Then ROIs were drawn on the basis of anat datasets.And I had spent too much time on drawing these ROIs.
Now a few days after that, the data is analyzed using a new pipeline: auto block,tshift,resample,despike,align,tlrc,volreg,mask,scale and regress.That is, tshift is done additionally just after auto block and the functional datasets are resampled to anat and blur isn’t done to keep the higher resolution.I know the ROIs drawn before will not fit the functional datesets with new analysis any more.But I really want to save my time to find methods for transforming the ROIs drawn on the anat which was aligned to the old functional datesets in previous analysis to fit the new functional datasets.
Thank you!
Jogi

2

Hi Jogi,

Were the ROIs drawn on the original space anatomy or the
standard space one?

Keep in mind that regardless of the processing done to the
EPI, the ROIs are aligned to a particular anat. So all you
have to worry about is what happens to the anat.

  • rick
3

Hi Rick,
The ROIs were drawn on the old dataset '*_ns+tlrc’ in tlrc space which seemed to have been aligned to the EPI in the steps of align or volreg in previous analysis using uber_subject.py. I think these ROIs couldn’t match the new anat datasets '*_ns+tlrc’ or EPIs any more. Because the new anat datasets '*_ns+tlrc’ were aligned to the EPIs with new analyis: tshift and resample were done additionally to the new EPIs before align,tlrc and volreg.
Thank you!
Jogi

4

Hi Jogi,

There should be a tiny difference in EPI to
anat alignment of course, but I would expect
the registration of the anat to the template to
be identical, meaning the ROIs should still
be in alignment.

Did you actually compare these in the afni
GUI? Did you compare the final_anat+tlrc
dataset between the two methods, and how
the ROI overlays them?

  • rick
5

Hi Rick,
I compare the data of one subject as representative.I can see only tiny difference at the outer contour of the brain on final_anat+tlrc between the two methods.And the ROI seems to overlay both the old and new anat dataset well.But I am worried about some key difference can’t be seen by the naked eyes.And the key difference can’t be seen can cause bad overlaying between the old ROI and new anat.
Thank you!