Hi AFNI/FATCAT experts, Sorry that after construction of my analytic pipeline, I encountered an unexpected problem. I found that the Tortoise output by AFNI Export has (0,0,0) coordinate at the bottom left of the image, not in the center of volume (AFNI convention). It seems that 3dwarp (adding translation to volume) and vecwarp (adding constants to gradient file) could serve as a quick fix. However, I'd like to inquire:

1. Would different coordinate systems influence FATCAT? Is (0,0,0) at the center of volume a per-requisite for FATCAT to work properly? (I've checked that the FATCAT_Demo AVEB0_DWI.nii.gz has (0,0,0) at the center of volume)

2. Is there any simple option provided by Tortoise to handle this? Since calcvm is equipped with AFNI Export, it would be sensible that the outputs have already conformed to AFNI convention.

On [science.nichd.nih.gov], there are several lines relevant to my question but I have no idea where to work on that. I cite as below:
"A new option to change the orientation of the imported images added. This "Original Image Axis for flipping" can change the axes of the original image to whichever orientation the user needs. The B-matrix is rotated accordingly. The orientation convention of DIFF_PREP is as follows:
The (0,0,0) coordinate of the image is the bottom left of the image (instead of top left as in ITK convention). The standard orientation is from left of the image to right: right to left anatomical, bottom to top of the image is posterior-anterior anatomical, increasing slice number is superior. Therefore in our standard orientation convention, our framework is 'LAS'.
With this new reorientation tool, the users can provide the original orientation of the image (for example 'ASL' for sagittal) and the images and the B-matrix will be transposed to DIFF_PREP's standard convention, 'LAS'."

I appreciate further help and comment, JoJo ~