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 Isuspect
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 commandmris_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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