Hi Matt,
XTRACT expects a non-linear transform between subject and standard space, because a linear transform is usually not accurate enough to match a subject's data to standard space. So, it is looking for a file like standard2diff.nii.gz, not standard2diff.mat.
You can create such a non-linear transform by running FNIRT, which you can initialise with your linear transform. You will also have to create the inverse transform by running `invwarp`.
Good luck,
Michiel
> On 29 Aug 2022, at 21:36, Matthew Amandola <[log in to unmask]> wrote:
>
> Hi,
>
> Currently, I am attempting to run XTRACT on one of my datasets. In my xfms directory, I have a standard2diff.mat file, and I've even used it to transform some standardized ROI's into individual space for testing. However, when I attempt to use xtract with the following command:
>
> xtract -bpx $BPX_DIRECTORY -out $OUTPUT_DIRECTORY -species HUMAN -native
>
> I receive the following error:
>
> "Image $BPX_DIRECTORY/xfms/standard2diff not found"
>
> I receive the same error when also trying to run XTRACT in standardized space. Does anyone know a solution for this?
>
> Thank you!
> - Matt
>
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