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Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| 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
" is thrown.
I highly appreciate your help here!
Bests,
Philipp
Edited 1 time(s). Last edit at 04/27/2022 04:00PM by philippn.
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.
