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Sounds like you had a clinical scan and got a copy of a sagittal scan series and an axial scan series. Those would be "2D" acquisitions in which the slice thickness is probably considerably thicker than the in-plane resolution. That kind of data isn't
ideal for FS. Rather, data for FS is usually collected with what is known as a "3D" sequence, and acquired with isotropic resolution in all 3 axes, typically 1 mm resolution or less.
You're free to try using the AX series if you wish, although it will likely still have "issues" as well.
cheers,
-MH
--
Michael Harms, Ph.D.
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Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Alexander van Dijk <navare...@gmail.com>
Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, August 26, 2015 1:27 PM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] how to fix errors in 3d mesh
Hi all,
I am an interested neuroscience newbie and I am following this excellent online guide on how to create a 3d print of my cortex using an MRI scan and freesurfer: http://nmarinsek.com/3D-printed-brain/
Sofar, i have been successful in generating the left and right hemispheres based on an eSAG T1 MRI scan (3T) of 32 images, but the right hemisphere appears to have a large hole in the 3d mesh and in general seems to be of less fidelity than the
left hemisphere:
I am wondering what could be the cause of the gap, the lower fidelty in general, and how best to fix it?
Also, after the MRI scan I received both the eSAG T1 scan (32 images), and an eAX T1 (36 images). Would there be any reason to use one over the other, and is it possible to combine these in freesurfer for better quality modeling?
Thank you,
Alexander
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