It works but the magic number now is 2067208 and read_surf still does not read it
On Mon, Feb 29, 2016 at 7:52 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > try this version > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize > > > On 02/23/2016 10:17 AM, Maheen Siddiqui wrote: > > I changed the directory and it ran, but with errors. I had to change > > the last part --surf lh.seghead --surf-smooth 10 because it does not > > recognise --surf. When I change this to --o, it runs but with errors. > > > > On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > > > On 2/23/16 9:39 AM, Maheen Siddiqui wrote: > >> It seems to be giving me an error and saying it cannot read the > >> seghead.mgz file. > > Is it in the same directory where you are running the command? If > > so, what is the terminal output? > >> > >> From my earlier question; do you know how to check if lh.seghead > >> is corrupted? > > If you can view it in tksurfer/freeview, then it is probably not > > corrupted. I vaguely remember that there was some problem reading > > this file in matlab, but I don't remember every coming up with a fix > > > >> > >> On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve > >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > wrote: > >> > >> you can try > >> > >> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead > >> --surf-smooth 10 > >> > >> > >> > >> > >> On 2/23/16 9:22 AM, Maheen Siddiqui wrote: > >>> Is it possible to use a different function? Can I use > >>> mri_vol2surf on the seghead.mgz file? Or do you think that > >>> mkheadsurf is the right one to be using? > >>> > >>> Thanks!! > >>> > >>> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve > >>> <gr...@nmr.mgh.harvard.edu > >>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > >>> > >>> Can you load it in tksurfer or freeview? > >>> > >>> > >>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote: > >>>> Hi FreeSurfer users, > >>>> > >>>> I have used the "mkheadsurf" command to create a head > >>>> surface for my subject. However when I try to use > >>>> "read_surf" to read the "lh.seghead" file that is > >>>> created, the magic number is not one that is recognised. > >>>> > >>>> Having read some previous posts/questions with similar > >>>> problem/error, I think the problem is probably within > >>>> the "lh.seghead" file. I think someone wrote that > >>>> incompatibility of the magic number means that the > >>>> surface is corrupted. Is there a way to check errors of > >>>> mkheadsurf? Or whether something is wrong? It looked > >>>> fine in freeview. > >>>> > >>>> Does anybody have any advice? > >>>> > >>>> Thanks, > >>>> > >>>> Maheen > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> <mailto: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. > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto: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. > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > 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. > > > > > > > > > > _______________________________________________ > > 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 >
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