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> 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> > 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>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 >>> 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 . 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 . 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 . 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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