Hello,

I have a dataset with very oblique functional runs for almost all subjects. The first/upper image below shoes the original (raw data) anatomical-functional overlap.

Then, I ran 3drefit on both the anatomical and functional scans as follows:

3dcopy $directory_raw/anat/T1w.nii.gz Temporary
3drefit -oblique_recenter Temporary+orig
3drefit -deoblique Temporary+orig
3dcopy Temporary+orig Anat_deoblique
rm Temporary+orig.BRIK
rm Temporary+orig.HEAD

3dcopy $directory_raw/task/task.nii.gz Temporary
3drefit -oblique_recenter Temporary+orig
3drefit -deoblique Temporary+orig
3dcopy Temporary+orig Task_deoblique
rm Temporary+orig.BRIK
rm Temporary+orig.HEAD

The second image below shows the new anatomical-functional overlap for the same subject after running the code above. It looks better, but the overlap is still not nice. I get these bad results for most of the subjects.

Question: What further options are recommended to improve the overlap berfore I start preprocessing the data with AFNI proc? I would like to get a nicer overlap first, since the functional run is still kinda oblique even after running 3drefit.



Edited 1 time(s). Last edit at 12/12/2022 09:02AM by Philipp.