Dear Sarah,
You are absolutely right that --useReconMNI partially removes pose from the segmentations. The affine MNI registration used for this is estimated using a subcortical mask, and this means that pose of the entire complex of subcortical structures (plus brainstem) is removed, but not the relative pose of the individual structures. The latter type of variations in pose can be removed with --useRigidAlign.
Hope that helps!
Best,
Eelke
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Sarah Hirsiger
Sent: 14 March 2017 17:56
To: [log in to unmask]
Subject: [FSL] FSL FIRST use --useRigidAlign?
Dear FSL-Experts
I anticipate to conduct a FSL-FIRST analysis and was screening the FSL mailing list for advice.
Based on the FIRST UserGuide you could either reconstruct the meshes in the native space of the images with [--useReconNative --useRigidAlign ] or in MNI space with [—useReconMNI].
Additionally, there is noted that to remove pose from the meshes you should use —useRigidAlign (with either --useReconNative or --useReconMNI)
Does this mean that if I am not interested in pose of a structure I should run --useReconMNI WITH --useRigidAlign?
This seems not straight forward to me as I would assume that the transformation to MNI space would already take care of this?
Thanks a lot for your help
Sarah
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