Reslice image to template without changing transform

preprocessing

#1

I have an ROI (nii.gz) in the correct orientation (pre-registered to the T1w) however, it has a few more axial slices than the T1w image I am overlaying it on. I use ‘mrtransform -template’ to regrid the ROI, and it ultimately changes its orientation (transform).

Is there a way to regrid without repositioning? I attempted to use ‘mrcop’ to simply remove a few axial slices - but this shifts the ROI axially - which isn’t great.

Many thanks - Jamie


#2

I’m not sure I understand exactly what the problem is. Would you mind posting the output of mrinfo on the relevant files (ROI & T1w) before and after regridding, so we can see what the changes are that are problematic?

Also, when you say it shifts the ROI, how are you determining that? Does it shift when displayed in mrview, or in fslview (I’d expect the two to behave differently here).


#3

Apologies for the slow response time. I am using MRtrix and DSI studio to visualize the ROIs. After regridding the CST ROI (saved as an nii.gz for viewing purposes) would be shrunken and shifted (strangely).

I resolved the issue by re-gridding earlier in the processing pipeline. I’ll look to recreate the issue and post the mrinfo you asked for.