Keren. You can rotate them manually if you can figure out sin/cos in an affine matrix.
However, a good strategy is to use flirt with -dof 6 with an average template (MNI, or other) or another MRI that is in the correct orientation. -dof 6 will do a rigid registration (rotation, translate) without modifying the original size or shape (size, warp).
John
***********************************************
John E. Richards
Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC 29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: [log in to unmask]
HTTP: jerlab.psych.sc.edu
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-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Keren Lesinger
Sent: Sunday, September 10, 2017 9:28 AM
To: [log in to unmask]
Subject: [FSL] oblique anatomical images
Hi
I have anatomical images from an open datasource. Currently, I ran fsl_anat on the anatomical scans without registration to MNI (in the near future I am interested in creating my own anatomical common space using ANTs, therefore I skipped the MNI registration). Some of the original images are a little bit oblique and even though I ran fslreorient2std as part fsl_anat the output remained oblique, how is it possible to deoblique the anatomical scans without registration to MNI?
Thanks in advance,
Keren
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