Dear FSL users,
I am looking for assistance with evaluating the quality of backwarping of ROIs from standard space into native space. I used Featquery with a mask from the Harvard-Oxford atlas to extract ROI data. Because Featquery warps the mask from standard space back into each participant's native space, I now want to evaluate the accuracy of the backwarping (i.e., overlay the backwarped mask onto the subject's highres for quality control).
Does Featquery save the backwarped mask, or is there a certain command I should use to warp the standard-space mask to each subject's space? I didn't find a saved mask, so I've been using applywarp to try to apply the inverse of the transformation matrix from the subject's initial registration to the standard-space mask. The threads on applywarp and invwarp have been helpful, but I am still getting errors during this process. This is what I'm trying, where standard2highres.mat is from the subject's first level registration directory:
applywarp -i HarvardOxfordmask.nii.gz -o HarvardOxfordmask_tonativespace -r T2highres.nii.gz -w standard2highres.mat
Error: ** ERROR (nifti_image_read): failed to find header file for 'standard2highres.mat'
I get the same error when I try to use an inverse transformation matrix calculated using invwarp or convert_xfm.
Thanks very much for any suggestions.
Best,
Dylan
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Dylan G. Gee, M.A.
University of California, Los Angeles
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