Try adding --projfrac 0.5
On 10/12/2016 11:29 AM, Crawford, Anna wrote: > I did: > > mri_vol2surf --src > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMnn.mgz > --out > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMnnS.mgh > --regheader segfs --hemi lh --surf white --out_type mgh --fixtkreg > > which resulted in the same type of surface. I looked at the volume and it > seemed as though things were labeled correctly. The images are attached. > > 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: Wednesday, October 12, 2016 10:47 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Remapping Volume > > 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 > > =================================== > > > 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
