That seems to have worked and the regions are solid now. Thank you!
Anna ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, October 12, 2016 2:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Remapping Volume 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. 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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 =================================== 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
