Re: [Freesurfer] mris_flatten error: bad vertex

Hi Foteini we need a lot more information. How did you create the patch? What was your command line and full screen output? What version of FS are you using? cheers Bruce On Tue, 20 Feb 2018, Foteini Protopapa wrote: > Dear FreeSurfer Experts, > > > Can somebody tell me if there is a solution

Re: [Freesurfer] mris_flatten error: bad vertex

Dear FreeSurfer Experts, Can somebody tell me if there is a solution to this mris_flatten error? I get... MRISreadPatch: bad vertex # (144585) found in patch file and is not about how I save my patch or where. I have done it another 82 times and everything worked perfectly. Any insights/

Re: [Freesurfer] mris_flatten error

Dear. All. I tried tksurfer and it works.. It's still very strange why tksurfer-sess does not work. The command line that worked successfully is: tksurfer replay06 lh inflated -curv -gray Then I overlayed the contrast result sig.nii.gz and the registration file. Then I cut the plane and then

Re: [Freesurfer] mris_flatten error

Oh, 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 Then I select 3 points along a boundary between upper and lower visual fields (near calcarine sulcus) and press "Cut line". Then,

Re: [Freesurfer] mris_flatten error

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.

Re: [Freesurfer] mris_flatten error

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

Re: [Freesurfer] mris_flatten error

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

Re: [Freesurfer] mris_flatten error

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

Re: [Freesurfer] mris_flatten error

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:

Re: [Freesurfer] mris_flatten error

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

Re: [Freesurfer] mris_flatten error

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

[Freesurfer] mris_flatten error

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

Re: [Freesurfer] mris_flatten error: bad vertex

Hi Ji that does sound strange! Can you tar and gzip the subject and upload it to our website so I can see if I can replicate the problem? cheers Bruce On Thu, 17 Mar 2016, Ji Won Bang wrote: > Dear. Freesurfer experts. > > Hi. > > I'm having a problem with mris_flatten (version 5.3.0) > >

Re: [Freesurfer] mris_flatten error: bad vertex

Dear. Bruce. Thanks a lot for your help! I attached the tar.gz file for mri below. If you need anything more, let me know. Thanks, Ji Won​ replay06_mri.tar.gz ​ 2016-03-17 11:40 GMT-04:00 Bruce Fischl

[Freesurfer] mris_flatten error: bad vertex

Dear. Freesurfer experts. Hi. I'm having a problem with mris_flatten (version 5.3.0) Could you please help me fix this problem? My 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 It returns the error: