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April 27, 2022 03:58PM
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 moody smiley" is thrown.

I highly appreciate your help here!

Bests,
Philipp



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

3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

philippn April 27, 2022 03:58PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

rick reynolds April 27, 2022 04:14PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley Attachments

philippn April 27, 2022 05:14PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

rick reynolds April 27, 2022 05:21PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

ptaylor April 27, 2022 05:24PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

philippn April 27, 2022 06:26PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

ptaylor April 28, 2022 07:29AM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

philippn April 28, 2022 11:35AM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

ptaylor April 28, 2022 12:31PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

philippn April 28, 2022 07:17PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

ptaylor April 29, 2022 08:52AM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

philippn April 29, 2022 04:04PM



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