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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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Hi, ptaylor,
The mag data and CEST data both look "correct" and only 3dinfo showed different orientation. I used fslswapdim to make both of them have same orientation (RIP) in AFNI view and 3dinfo. I tried plug-nodge to manually rotate CEST to align it to mag image,but failed. Is there other better way to align CEST (part of brain) to mag image (whole brain)?
by
Tracy_AFNI
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AFNI Message Board
Hi, Ptaylor,
Thanks for your reply!
I ran the script what your suggested and got the followed result:
3dinfo -is_oblique mag_res_brain.nii.gz
0
3dinfo -is_oblique CEST_res_brain.nii.gz
0
I tried other way to rotate the mag to match the CEST orientation, then align mag to CEST with 3dresample -master CEST.nii -prefix mag_to_CEST.nii -inset mag.nii, is this right one to align mag to CES
by
Tracy_AFNI
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AFNI Message Board
Hi,
I'm frustrated the 3drefit function for a while:
I have a field map data (I extract magnitude(mag) image and the mag image 3dinfo showed orientation is SAR) and a CEST data (3dinfo showed orientation LSP) from rat brain and try to run the field map correction for the CEST image.
I resample them to 4x4x4 with
3dresample -dxyz 4 4 4 -prefix mag_res_brain444.nii -inset mag_res_bra
by
Tracy_AFNI
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AFNI Message Board