no, for all surfaces for the same hemi (lh and rh). lh.inflated.K is not
a surface - it's a scalar field over the surface. The ones that should be
the same are:
lh.inflated
lh.white
lh.pial
lh.orig
lh.sphere
lh.sphere.reg
and same for the rh (but different from the lh ones)
cheers
Bruce
On Tue, 22 Mar 2016, Ji Won Bang wrote:
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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