Dear Paul,

thank you.
I read on Andy’s Brain Blog (https://www.andysbrainblog.com/andysbrainblog/tag/3dUndump) that AFNI’s xyz coordinates correspond to MNI152’s x -y z.
More precisely, the positive y value in AFNI’s xyz coordinates corresponds to a negative y value in MNI152 (and vice versa).

So I went back to my Python script that initially loads the output of 3dmaskdump. In Python, I multiplied the y coordinates (extracted from AFNI) with -1.

y = y * -1

Then, I ran 3dUndump again, but with the multiplied y-coordinate values.
Now, the code you provided me yields no mismatch:

3dinfo \
-same_all_grid \
-prefix Extracted_ACW_Awake.nii Resample_Yeo7N_1000ribbon.nii

prints

NO-DSET	NO-DSET	NO-DSET	NO-DSET	NO-DSET	NO-DSET
0	0	0	0	0	Resample_Yeo7N_1000ribbon.nii

The attached image below shows a visual comparison between both files. The visual inspection shows that there are still some slight mismatches.
The cortical grey matter looks more thick in the resampled atlas version than in the functional measurement-based result (of course, I used the same 1000 parcels ribbon version in both cases!).
Based on the information that I provided so far, do you have any idea where the slight mismatches can come from?

At least the data looks to be identically positioned in space, after multiplying the y-coordinates with -1.

Thanks so far.



Edited 1 time(s). Last edit at 04/10/2023 01:03PM by Philipp.