afni.nimh.nih.gov

Hi all,

I want to warp ROIs from an atlas to a native image space, which only consists of several slices covering the upper part of the brainstem. To this end, I aligned the native image to a native structural image using align_epi_anat.py resulting in a native_al+orig and a native_al_mat.aff12.1D file .
Next, I aligned the atlas space MNI template image to the structural image using @SUMA_AlignToExperiment resulting in a MNI152_T1_1mm_brain_Alnd_Exp+orig and MNI152_T1_1mm_brain_Alnd_Exp.A2E.1D files.
Finally, to warp individual ROIs from the atlas template space to native space, I want to use 3dNwarpApply with the following call:
3dNwarpApply -nwarp native_al_mat.aff12.1D -source atlas_ROI.nii -master native_image.nii -prefix ROI_in_native_space

However, when I run this command, the error: 3dNwarpApply error "Warp dataset 'native_al_mat.aff12.1D' name is too much like a matrix text file " is thrown.

I highly appreciate your help here!

Bests,
Philipp



Edited 1 time(s). Last edit at 04/27/2022 04:00PM by philippn.