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philippn
April 27, 2022 05:14PM
Hi Rick,

thanks for your fast response!

I followed your advice and called 3dAllineate with the following command:

3dAllineate -prefix ROI_in_native_space -base native_image.nii -source atlas_ROI.nii -twopass -cost lpa -1Dmatrix_apply native_al_mat.aff12.1D -autoweight -cmass -twobest MAX

The good news is that the program worked. The bad news is that the ROI is far off from where it should be (see image attached).

Did I miss something here?

Bests,
Philipp
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open | download - ROI_in_native_space.JPG (70.8 KB)
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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