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-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@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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hereby notified that any dissemination, distribution or copying of this 
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