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Dear AFNI users-

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

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shjung
February 06, 2023 01:41PM
Hello, AFNI experts,


May I get pieces of advice for aligning turbo-spin echo to the T1 3d image?


3dWarp -verb -card2oblique AK_expvol+orig -prefix AK_expvol02_deobl+orig AK_expvol02+orig

align_epi_anat.py \
-anat AK_expvol+orig \
-epi AK_expvol02_deobl+orig \
-epi_base 5 \
-epi2anat \
-volreg off \
-anat_has_skull yes \
-deoblique off \
-suffix _al_aligned



As the script depicts, a partial 3d image (TSE, AK_expvol02) was deoblique processed. And then, it was aligned to the T1 image (AK_expvol+orig). However, the alignment was not successful, as you can see in the screenshot. In this case, what can I try to align perfectly?

As you can see in some screenshots, the two 3d images have a different gap between the voxels. Is the different size of the voxel gap across two different 3d images the matter?



Edited 1 time(s). Last edit at 02/06/2023 01:53PM by shjung.
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Attachments:
open | download - Aligned_brain.png (1.88 MB)
open | download - Screenshot 2023-02-06 at 12.40.29.png (1.78 MB)
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Subject Author Posted

How can I align a partial 3d image (Turbo-spin echo) to a whole brain 3d image (T1)? Attachments

shjung February 06, 2023 01:41PM

Re: How can I align a partial 3d image (Turbo-spin echo) to a whole brain 3d image (T1)?

Daniel Glen February 07, 2023 11:16AM

Re: How can I align a partial 3d image (Turbo-spin echo) to a whole brain 3d image (T1)? Attachments

shjung February 08, 2023 02:17PM

Re: How can I align a partial 3d image (Turbo-spin echo) to a whole brain 3d image (T1)?

Daniel Glen February 08, 2023 11:33PM