Hello experts,

I am using AFNI to preprocess resting state data from the ADNI database. Prior to running the pipeline, I checked the orientation of each of my files that would be input to the proc.py script for each subject using the "3dinfo -oreint" command. I found that the T1 data was in LPI, resting state in RPI, and WM/vent masks generated in freesurfer were in RSP. Prior to running the proc.py scripts, I resampled the resting state data and the freesurfer data to be in LPI to match each other and the structural images. I proceeded to run the processing script in two ways:

1. Using the original data, in its original, non-resampled orientation
2. Using the LPI resampled data

Interestingly, when I ran the pipeline using the data that was not resampled, only a few subjects were flagged during the CHECK_FLIP portion of the script. This flip error went away when I used the LPI images as input.

However, an additional problem came up. When I ran the processing pipeline with the LPI resampled images, the script errored out for 10% of my sample with the following error:
3dpc -mask follow_ROI_FSvent+tlrc -pcsave 3 -prefix rm.ROIPC.FSvent.r01 rm.det_pcin_r01+tlrc
++ 3dpc: AFNI version=AFNI_19.2.01 (Jul 3 2019) [64-bit]
** FATAL ERROR: mask is all zeros!

It seems that when the LPI FSvent mask is eroded, no voxels survive but this does not occur with the RSP (non-resampled freesurfer images). Do you know why this would be? Additionally, would you recommend that I resample the images to be in LPI prior to running proc.py or to keep the resting state images and freeesurfer masks in their original orientation?

I really appreciate your help!
Jenna