Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.
Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org> wrote: > No problem. I'm not exactly sure, but I think I just want a surface > overlay so mri_vol2surf would be what I want. Right now, I am just trying > to get down the generic way of how to do it which is why I went with trying > to overlay the parcellation onto the inflated surface. Later, I will have > different modalities such as PET that I will want to overlay on the > inflated surface that will already be registered to the MRI. So I just > wanted to get the proper workflow of how to get a volume overlayed onto the > surface if that makes sense. > > Thank you, > Anna > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > *Sent:* Friday, September 30, 2016 10:48 AM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Volume to Surface > > Sorry - always helps to read the whole question :D > > So, you are trying to create an inflated white surface? As far as I know > this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and > inflated surfaces that are the pial pushed outwards. > > Also, "mri_vol2surf" creates surface overlays on surfaces that already > exist. > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org> wrote: > >> I already ran recall-all. I am trying to create a different surface not >> created using recon-all. >> >> Anna >> ------------------------------ >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna >> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] >> *Sent:* Friday, September 30, 2016 10:40 AM >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] Volume to Surface >> >> You have to run recon-all to get the surfaces of a volume. >> >> Trisanna >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org> wrote: >> >>> Hello, >>> >>> I am trying to take nay volume that is registered and create an inflated >>> surface. I am trying to use mri_vol2surf. I am having problems with the >>> registration source. From the examples I could fine, it should be --srcreg >>> *.dat. The only *.dat file I have is segment.dat which does not work. I >>> also tried using the white matter volume which also didn't work. My input >>> and output is below. Could you offer some guidance on the registration file? >>> >>> Thank you, >>> Anna >>> >>> mri_vol2surf --src /mnt/netScratch/crawforda/Brai >>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out >>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh >>> --srcreg >>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat >>> --hemi lh --surf white --out_type paint >>> INFO: output format is paint >>> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m >>> ri/wmparc.mgz >>> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m >>> ri/segment.dat >>> srcregold = 0 >>> srcwarp unspecified >>> surf = white >>> hemi = lh >>> reshape = 0 >>> interp = nearest >>> float2int = round >>> GetProjMax = 0 >>> INFO: float2int code = 0 >>> INFO: changing type to float >>> Done loading volume >>> regio_read_register(): Success >>> Error reading betplaneres from /mnt/netScratch/crawforda/Brai >>> nStem/study11074/S2sdt/segfs/mri/segment.dat >>> >>> =================================== >>> >>> 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 >> >> >> 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 > > > 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. > >
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