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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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