Dear. Bruce.
Thanks for your help.
When I tried:
mris_euler_number rh.inflated.K
It gave me:
nquads=15728644, nvertices=574
ERROR: MRISread: file 'rh.inflated.K' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!
When I tried:
mris_euler_number lh.inflated
It gave me:
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
F =2V-4: 289950 = 289954-4 (0)
2E=3F: 869850 = 869850 (0)
When I tried:
mris_euler_number rh.inflated
It gave me:
euler # = v-e+f = 2g-2: 147184 - 441546 + 294364 = 2 --> 0 holes
F =2V-4: 294364 = 294368-4 (0)
2E=3F: 883092 = 883092 (0)
So if everything is correct, I should see the same numbers for all
surfaces, but since it's not the case, I should run recon again...
Thanks,
Ji Won
2016-03-22 12:24 GMT-04:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
> you can try recon-all -make all for that subject and and see if it doesn
> anything. But run mris_euler_number on those surfaces and see if they
> match. They should all have the same number of faces/edges/vertices (for
> one hemisphere in the same subject)
>
> On Tue, 22 Mar 2016,
> Ji Won Bang wrote:
>
> > Dear. Bruce.
> >
> > Thank you for your advice.
> > I think I misunderstood what you meant.
> >
> > What I did is this.
> > I showed the contrast result on a surface by using the command:
> > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
> -contrast HorVer
> >
> > Then I cut line, and then plane (occipital plane) and save it(3d) as
> lh.oc.patch.3d
> > under $SUBJECTS_DIR/$SUBJECT/surf/
> >
> > I'm not sure if I regenerated the surface files correctly but I believe
> I created the
> > surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all process.
> >
> >
> > Should I do something else to regenerate the surface?
> >
> > Thank you.
> >
> > Best,
> > Ji Won
> >
> >
> >
> >
> >
> > 2016-03-22 11:39 GMT-04:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
> > what surface did you recut it from? Can you run mris_euler_number
> on that
> > surface (presumably the inflated) and also on the white/orig/pial
> > surfaces? They should all have the same number of vertices, but I
> suspect
> > some of them won't, meaning that they need to be regenerated.
> >
> > cheers
> > Bruce
> >
> >
> >
> >
> > On Tue, 22 Mar 2016, Ji Won Bang wrote:
> >
> > > Dear. Freesurfer experts.
> > >
> > > Hi. How are you?
> > >
> > > I'm trying to flatten the visual cortex using the command
> mris_flatten
> > (freesurfer
> > > version 5.3.0).
> > >
> > > The command line is:
> > > mris_flatten -w 0 -distances 12 7
> > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
> > > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat
> > >
> > > The error I get is:
> > > using write iterations = 0
> > > sampling 7 neighbors out to a distance of 12 mm
> > > reading patch
> > /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with
> > > 27964 vertices (19.0% of total)
> > > MRISreadPatch: bad vertex # (147220) found in patch file
> > > No such file or directory
> > >
> > > Previously, Bruce advised me to recut it, so I deleted the
> > lh.oc.patch.3d and recut
> > > it. However, freesurfer gives me the same error message...
> > >
> > > Could you please help me fix it?
> > >
> > > Thank you so much.
> > >
> > > Best,
> > > Ji Won
> > >
> > >
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