Hi,

Thanks for your reply. Again, I'm still very new to AFNI but what we are trying to do is to simply analyze the resting state data (does not include the other runs). We are still in the initial stages of preprocessing the Oblique T1 MPRAGE (anat data) and the resting state Oblique Axial ep2d bold data (EPI data).

Currently our issue with the first 3 lines is that we have both an oblique anat and functional dataset. From my understanding, we have to fix the obliquity of our anat and create a straight anatomical reference to enable support for our oblique functional. The -rotyourself will rotate our oblique anatomical to *itself* rather than a straight anatomical since we don't have a straight anatomical reference (normally we would use -rotobrick). However, when we try to apply our oblique functional on this now "straight" anat (using the -rotobrick function to process the functional using the processed anatomical as the -rotobrick reference), an error occurs stating that: "ERROR: Failed to handle oblique (tolerance exceeded)."

We've already applied the maximum tolerance possible as stated, but still we are receiving these errors and preferably we would like not to use any tolerance at all.

This is all prior to performing slice timing, motion correction, spatial normalization, and smoothing. We tried experimenting with it by adding 3dWarp functions which ended up running with no problems. However, when we check for coregistration between our anat and epi, the alignment is very off so we think this issue is in regards to the obliquity at the start of our preprocessing and less to do with the slice timing, moco, normalization, etc.

Again, still very new to AFNI but I'll check out this DIMON program and see if there is anything there that can help us with this obliquity problem. Any other tips / helpful advice would be very much appreciated!

Thanks!!