Hi

We’ve seen this recently on the list and it seems to have to do with Ants perhaps not keeping some header information used within probtrackx2. One quick fix is to use fslcpgeom to re-introduce the correct header information in your transformed seed masks.

Cheers
Saad

> On 31 May 2019, at 15:20, Marvin Jüchtern <[log in to unmask]> wrote:
>
> Dear community,
>
> I have a question about an error I get when running Probtrackx for a DTI tractography with seed ROIs together with termination and classification masks.
>
> My approach is a combination of Flirt and ANTs co-registration. My path is the following:
>
> bet struc.nii struc_brain.nii.gz -m -R
> flirt -in struc_brain.nii.gz -ref b0_unwarped_brain.nii.gz -omat struc2b0
> flirt -in struc_brain.nii.gz -out strucb0 -ref b0_unwarped_brain.nii.gz -applyxfm -init struc2b0
> ants.sh 3 template.nii strucb0.nii.gz ANTS_ 30x90x20 all_rois.nii.gz
>
> And then I split the registered file all_rois into all individual ROIs so I can run tractography on every one of them.
> After that I flirt a termination mask (Grey matter) on my strucb0-brain so that I can use it for my tractography.
> But when using the bedpostx-folder, a seed ROI (no matter which), the termination mask and some targets, I get this error immediately after starting the tractography:
>
> error: inv(): matrix appears to be singular
>
> I already checked the individual files, but can't find any errors in them.
> Do you have any suggestions what the problem could be? Is there anything I need to mention when using Probtrackx for this approach?
>
> Help is very much appreciated!
>
> With kind regards,
>
> Marvin, Clinical Cognition Sciences, UK Aachen, Germany
>
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