try including --out_type mgh and naming your output something like lh.wmparc.mgz
cheers Bruce On Fri, 30 Sep 2016, Crawford, Anna wrote: > Thank you! So good news, that worked and created wmparcSlh.w > > I'm not sure what the .w means. When I try to load it onto the surface, I > get an error: "Failed to load Surface overlay." > > 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 12:51 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Volume to Surface > > 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/BrainStem/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.r > eg --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.r > eg > 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/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.r > eg > > ____________________________________________________________________________ > 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/BrainStem/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/mri/wmparc.mgz > srcreg = > > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/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/BrainStem/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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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. > > > =================================== > > 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
