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 <fis...@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 <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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