My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org> wrote: > Yeah, I get Error: Option unknown for --regmethod > > 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 12:41 PM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Volume to Surface > > hmmm, yup not sure there. Did you try "--regmethod subject" > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org> wrote: > >> Just to make sure I am actually doing what you are suggesting my input >> and output is below. >> >> Thanks, >> 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 >> --reg >> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg >> --hemi lh --surf white --out_type paint >> INFO: output format is paint >> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/ >> mri/wmparc.mgz >> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/ >> surf/lh.sphere.reg >> 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 inplaneres from /mnt/netScratch/crawforda/Brai >> nStem/study11074/S2sdt/segfs/surf/lh.sphere.reg >> ------------------------------ >> *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 12:08 PM >> >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] Volume to Surface >> >> Did you try --regmethod subjid? or --reg sphere.reg ? >> >> If that doesn't work then I'm not sure how to help - Bruce or Doug, any >> thoughts? >> >> Trisanna >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org> >> wrote: >> >>> I am still having problems. If I do --reg subject I get an error back >>> that it is a directory. If I pick a specific file such as orig.mgz (default >>> according to help file), I get the same error as before. >>> >>> Thanks, >>> 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 11:04 AM >>> >>> *To:* Freesurfer support list >>> *Subject:* Re: [Freesurfer] Volume to Surface >>> >>> 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). 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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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