that seems ok, as I think the default is nearest neighbor. Can you visualize the volume you created and see if the incorrect labels are in it?
On Wed, 12 Oct 2016, Crawford, Anna wrote: > 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 >> >> =================================== >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by >> U.S.News & World Report (2015). Visit us online at >> http://www.clevelandclinic.org for a complete listing of our services, staff >> and locations. 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. >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News > & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of > our services, staff and locations. > > > 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. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
