Dear Chase,

have you changed any of the defaults (except writing the deformations) such as voxel-size or template? 

I had some trouble with the deformations in the past, but was sure to already solve that. Maybe you can send me one dataset (with batch file of your settings) so I can test this. Wi will send you an upload link...

Best,

Christian

On Fri, 9 Mar 2018 16:41:38 -0500, Chase Figley <[log in to unmask]> wrote:

>Dear SPM12/CAT12 Experts:
>
>I am stuck on what should be a pretty easy task, and am therefore hoping
>someone might be able to offer a fairly simple solution that I must be
>overlooking.
>
>I am trying to nonlinearly normalize rs-fMRI data from a patient population
>by first normalizing each participant's T1w images using CAT12 (and saving
>both the forward and inverse deformation fields), and then applying the
>forward deformation to the rs-fMRI data.
>
>So far, I have been trying to do this using "CAT12: Segmentation" (to
>generate the deformation fields), followed by "Apply Deformations (many
>images)", but something about what I am doing is not quite right. In case
>it matters, Matlab / SPM12 / CAT12 versions = 8.5 (2015a) / 6470 / 1278.
>
>Although the CAT12: Segmentation batch runs to the end (and the normalized
>images obtained directly from CAT12 segmentation appear to be correctly
>warped - i.e., by selecting "Yes" for writing out the modulated and
>normalized images for GM, WM, and T1w images), applying the deformations to
>any other images using "Apply Deformations (many images)" produces strange
>looking images in which the brains are shrunken, offset, and clearly
>distorted...which implies that I am not saving the deformations correctly
>and/or not applying them correctly.
>
>In an attempt to troubleshoot what might be happening, I have tried
>applying the forward deformation to the original T1w image that was used as
>the input for CAT12 segmentation, and even the warped images from that look
>wrong...and similarly, applying the inverse deformation to the
>correctly-warped T1w image (saved out directly from the "CAT12:
>Segmentation" batch) fails to produce anything resembling the original T1w
>image.
>
>Has anyone else ever encountered this issue before and/or have any ideas
>about what I might be doing wrong?
>
>Thanks in advance,
>
>Chase
>