I used:
--src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMpostcent2.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMpostcent2S.mgh --regheader segfs --hemi lh --surf white --out_type mgh
From the help file online, it looks like --fixtkreg would be used for the nearest neighbor. What is the proper flag to set it to use nearest neighbor interpolation?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, October 11, 2016 10:29 PM To: Freesurfer support list Subject: Re: [Freesurfer] Remapping Volume
what was your vol2surf command line? Make sure that it is using nearest neighbor interpolation On Tue, 11 Oct 2016, Crawford, Anna wrote:
Hi,
I am trying to remap a volume. I am using aparc+aseg.mgz volume. I loaded it into Matlab using load_mgh. In Matlab I remap the volume to different values. For example, all original values of 1022 will become 200 and all 1030 values will become 150. (This is just an example, not necessarily these numbers.) I save a new aparc+asegNew.mgz file using save_mgh. I use the same M and mr_parms that I got when I loaded in the original file. I'm not sure what these mean or if I need to change them. Then I use mri_vol2surf to create a new surface overlay onto the inflated hemisphere. When I do this, each region such as post central gyrus is 2 colors spotted together instead of a solid color like in the original. I have attached pictures as an example of what the original and remapped looked like. I didn't change the location of values, just simple gave each value a new one. Why is the one value speckled throughout?
Thank you, Anna
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.