Hi-

Just to check-- what version of TORTOISE are you using?

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)

I will assume you are using the 'afni export' from DIFF_CALC? (And thus, you get 2 files: DWI.nii and BMTXT.txt? Or do you export something different?)

TORTOISE will output into what AFNI calls RPI coordinates, and will have a specific origin based on the voxel dimensions. For me, typically the orientation and origin of the post-TORTOISEd DWI set is:

$ 3dinfo -orient -o3 DWI.nii
RPI	-1.500000	-1.500000	1.500000

(NB: mri_info would call this 'LAS' orientation.)

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.

Well, TORTOISE just outputs with a single orientation and origin, always; it doesn't follow what is input. However, you can adjust this later on, if you wish, using AFNI commands of 3drefit, for example. I use a script that will refit the data to have the same orientation and origin as the T2w reference volume, and then do a bit of tracking for sanity checking. I can send it to you, if you want; but it would be useful to know what versions of TORTOISE and AFNI you are using first.

However, it should be noted that the output data itself isn't wrong or unusable-- it just doesn't match up (spatially or orientationally) to what was input. Tracking and everything still works perfectly fine in this space.

--pt