Greetings AFNI gurus,

I've recently been wading into the murky waters of slice timing correction, and I'm trying to establish a robust procedure to ensure that I always get the correct -tpattern string for 3dTshift, regardless of scanner manufacturer or image orientation (sadly I cannot rely on relevant slice timing tags being ported during the NIfTI conversion process).

From reading this forum post - [afni.nimh.nih.gov] - I think I've gotten the hang of it, but I would greatly appreciate some feedback as to whether I'm on the right track or not. The procedure I have in mind is:

1, From the scanner printout, ascertain slice acquisition pattern (interleaved, sequential, sequential starting from slice 1...)

2. Also from the printout, establish the location of DICOM slice zero (top or bottom of the subject's head).

3. Work out in which order the slices are stored on disk in NIfTI format (3dinfo -orient).

4. If there’s a disparity between how the slices were acquired from the scanner and how they are stored in NIfTI, apply a flip to the tpattern accordingly (e.g., if the scanner printout shows that the slices were acquired sequentially from foot to head, but 3dinfo shows that the NIfTI orientation for the z-plane is Superior to Inferior, -tpattern would need to be changed from seq+z to seq-z).

Does that sound about right? Am I missing anything? Any clarification would be greatly appreciated!

Best,

Rich

P.s., I am assuming that all volumes were acquired axially