Ji WonBest,Thank you.Is it normal?It calls fsaverage..such as:1 thing that's weird is when I run:This is the usual way that I've been doing...Then I select 3 points along a boundary between upper and lower visual fields (near calcarine sulcus) and press "Cut line". Then, select 4 points to define the cutting plane: 1 on lower side of the line, 2 on upper side of the line, 3 on the opposite surface (use rotation tool), and 4 to specify which portion of surface is kept, and press "Cur plane". File->Patch->Save Patch As {lh, rh}.oc.patch.3dOh, I see.I showed the contrast results on a surface using the command:
tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower
tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower
Reading source surface reg /home/jbang/Projects/replay/mri//replay06/surf/lh.sphere.reg
Loading source data
Reading target surface reg /home/jbang/Projects/replay/mri//fsaverage/surf/lh.sphere.reg
Done
Previously when everything went smooth, I think it did not call fsaverage.2016-03-22 13:06 GMT-04:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:then you must not have cut the patch from those surfaces. The error is about a vertex # in the patch (147220), which is larger than the total number of vertices in those surfaces (144977), so it's out of bounds. How did you do the cutting?
On Tue, 22 Mar 2016, Ji Won Bang wrote:
Oh, I see.
When I run all of these surfaces, it gave me the exactly same numbers...
[jbang@cpu156 surf]$ mris_euler_number lh.inflated
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
F =2V-4: 289950 = 289954-4 (0)
2E=3F: 869850 = 869850 (0)
total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.white
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
F =2V-4: 289950 = 289954-4 (0)
2E=3F: 869850 = 869850 (0)
total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.pial
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
F =2V-4: 289950 = 289954-4 (0)
2E=3F: 869850 = 869850 (0)
total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.orig
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
F =2V-4: 289950 = 289954-4 (0)
2E=3F: 869850 = 869850 (0)
total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.sphere
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
F =2V-4: 289950 = 289954-4 (0)
2E=3F: 869850 = 869850 (0)
total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.sphere.reg
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
F =2V-4: 289950 = 289954-4 (0)
2E=3F: 869850 = 869850 (0)
total defect index = 0
Thanks,
Ji Won
2016-03-22 12:59 GMT-04:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
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
<fischl@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
<fischl@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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