Dear Professor Bruce I'm just trying to convert lh.pial surface to the volume with the down below command but the output doesn't make any sense ( lh.voulme contains zero). Could you please help? Mris_volume topo_defect_after/surf/rh.pial
Thank you! On Tue, Sep 19, 2017 at 1:11 PM Fereshte <fereshte.ramez...@gmail.com> wrote: > > On Tue, Sep 19, 2017 at 11:51 AM Fereshte <fereshte.ramez...@gmail.com> > wrote: > >> I changed the FreeSurfer version to 6 and now i could find it. >> Thank you! >> Cheers >> >> On Sat, Sep 16, 2017 at 9:21 PM Douglas Greve <gr...@nmr.mgh.harvard.edu> >> wrote: >> >>> Is it not in $FREESURFER_HOME/bin ? What version are you using? >>> >>> On 9/16/17 12:05 PM, Fereshte wrote: >>> >>> Well i did ask if it was possible to obtain the volume of Pial surface >>> and here's the response; >>> >>> "sure, mris_volume will give you the interior volume of any closed >>> surface >>> using the divergence formula. Note that this is *not* the volume of the >>> ribbon but rather the volume of the entire interior" >>> >>> I can't see mris_volume in FreeSurfer commands. >>> >>> On Sat, Sep 16, 2017 at 8:09 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> >>>> sorry, can you clarify what your question is? >>>> >>>> On Sat, 16 Sep 2017, Fereshte >>>> wrote: >>>> >>>> > Dear FreeSurfer developers >>>> > I couldn't find the mentioned mris_volume in the commands. Shall i >>>> use mri_vol2surf or something? >>>> > Looking forward to hearing from you! >>>> > On Tue, Sep 5, 2017 at 9:46 AM Fereshte <fereshte.ramez...@gmail.com> >>>> wrote: >>>> > Hi Bruce, >>>> > Thank you for your replies. >>>> > Cheers >>>> > >>>> > On Tue, Sep 5, 2017 at 4:52 AM Bruce Fischl < >>>> fis...@nmr.mgh.harvard.edu> wrote: >>>> > Hi Fereshte >>>> > >>>> > the algorithm is documented in the recon1 1999 NeuroImage and >>>> 2000 PNAS >>>> > papers >>>> > >>>> > cheers >>>> > Bruce >>>> > On Mon, 4 Sep 2017, Fereshte wrote: >>>> > >>>> > > What's the algorithm used to expand inner cortical boundary ( >>>> to achieve the >>>> > outer cortical boundary >>>> > > in pial surface) in FreeSurfer? >>>> > > On Mon, Sep 4, 2017 at 9:58 PM Bruce Fischl < >>>> fis...@nmr.mgh.harvard.edu> wrote: >>>> > > it will give the interior volume of whatever surface >>>> you give it as a >>>> > > command line argument. >>>> > > >>>> > > On Mon, 4 Sep 2017, Fereshte >>>> > > wrote: >>>> > > >>>> > > > Using the Pial surface; Does it mean mris_volume will >>>> give the inner >>>> > cortical boundary >>>> > > of the >>>> > > > surface and not the outer boundary? >>>> > > > Sincerely, >>>> > > > Fereshte Ramezani >>>> > > > On Mon, Sep 4, 2017 at 9:53 PM Fereshte < >>>> fereshte.ramez...@gmail.com> >>>> > wrote: >>>> > > > >>>> > > > On Mon, Sep 4, 2017 at 6:46 PM Bruce Fischl >>>> > <fis...@nmr.mgh.harvard.edu> wrote: >>>> > > > sure, mris_volume will give you the interior >>>> volume of any closed >>>> > surface >>>> > > > using the divergence formula. Note that this is >>>> *not* the volume >>>> > of the >>>> > > > ribbon but rather the volume of the entire >>>> interior >>>> > > > >>>> > > > cheers >>>> > > > Bruce >>>> > > > >>>> > > > >>>> > > > On Mon, 4 Sep 2017, Fereshte wrote: >>>> > > > >>>> > > > > Hello FreeSurfer developersIs it possible to >>>> have the volume of >>>> > pial surface >>>> > > in >>>> > > > FreeSurfer? >>>> > > > > >>>> > > > >_______________________________________________ >>>> > > > 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 . 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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. >>>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://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 >>> >>> >>> 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 . 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