Hi, Fabian-

Great, thanks, I think that all clarifies the situation.

On a preliminary note, I see you are using NMT v1.2, but the the NMT v2.0 is available. See here for images and download information:
[afni.nimh.nih.gov]
... and this draft about its benefits of v2.0 (more useful reference coords/dimensions, sharper detail, has the CHARM associated with it as well as the D99, two macaque demos in AFNI exist for it, ...), which you might have seen already:
[afni.nimh.nih.gov]
and here are the pages for the macaque demos:
[afni.nimh.nih.gov]
And for most applications, I think using the lower-res 0.5mm isotropic NMT v2.0 makes a lot of sense-- certainly if it will be used as part of FMRI processing, because those voxel sizes will surely be much larger. Why spend all the processin time and computer space (the 0.25mm isotropic dsets are 8x larger), if you don't need it? (Of course, if you *do* need it, then use the higher res.)

The dataset is *not* oblique (the "obliquity" matrix is identity + no shift). And actually, I should have noticed this from your GUI screenshots, because there is the "Card" message on the righthand side of each image panel, which is an abbreviation for "data in Cardinal coordinates" and not oblique ones.

However, the input T1w volume is not well-centered around (x, y, z)=(0,0,0). This potentially causes trouble for the initial alignment, because the two datasets are so far off-- see this part of the AFNI Bootcamp alignment talks:
[youtu.be]
(and, in case it of interest, there are a lot more of these, too:
[www.youtube.com]
which might be useful, e.g., for curing any insomnia.)
On another practical note, having the datasets far-from-centered on the reference volume will create a problem when applying the warp field later, because it will have to be a huge dataset to cover a bit space (computer memory concerns-- might be too big for the RAM to handle, and so just fail with a "Killed" message).

How to address this? Well, in this particular case, there is a lot of non-brain material around, but we the center of the brain actually looks like it is in the center of the volume. Therefore, we can copy the dset and use this @Align_Centers command (where you provide your template name where TEMPLATE is written):

# copy dset
3dcopy T1w.nii.gz T1w_recent.nii.gz

# apply recentering to dset: edits dset directly (which is why we first copied)
# also stores shift in a separate file (*_shft.1D)
@Align_Centers      \
     -grid                    \
     -no_cp                \
     -dset T1w_recent.nii.gz \
     -base TEMPLATE

If you run the new T1w_recent.nii.gz through the script to check for overlap, how does *this* one look?

And I will ask, what kind of analysis are you doing with this dataset? Do you have other data (like FMRI) that is aligned with this subject's anatomical? If so, we might want to shift that, similarly.

--pt



Edited 1 time(s). Last edit at 10/07/2020 10:34AM by ptaylor.