AFNI Message Board

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

History of AFNI updates  

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Daniel Glen
July 22, 2010 12:33PM
I haven't seen the gantry tilt before, but someone had dealt with the DICOM files in Matlab.

[www.mathworks.com]
[www.mathworks.com]

I tried a couple things in AFNI that might be right (but they might be wrong too).

3dWarp -deoblique -prefix ct_rot_deob ANATOMIC-NO_GROUP-CT-3-2+orig.
3dcopy ct_rot_deob+orig. ct_rot_deob_fix3
3drefit -ydel `ccalc 'tand(30)*0.5` ct_rot_deob_fix3+orig.

The result looks roughly right, but it's hard to know for sure. The standard DICOM parameters you mentioned do contain the 30 degree information, but it needed a bit more attention to handle an additional shearing and not just a rotation. Here I deobliqued the data by tilting the data back from its 30 degrees and then adjusted the voxel size in the y-dimension to compensate for the distortion. You may want to align this to an MRI structural image. Since this image is mostly skull, you might try aligning to just the skull image in the MRI possibly using 3dSkullStrip and 3dcalc and then align_epi_anat.py.
Subject Author Posted

Gantry Tilt

Chad July 08, 2010 04:30PM

Re: Gantry Tilt

Daniel Glen July 08, 2010 05:08PM

Re: Gantry Tilt

Chad July 08, 2010 05:38PM

Re: Gantry Tilt

Daniel Glen July 08, 2010 06:03PM

Re: Gantry Tilt

Chad July 09, 2010 09:04AM

Re: Gantry Tilt

Daniel Glen July 22, 2010 12:33PM

Re: Gantry Tilt

Chad July 23, 2010 11:46AM