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 <https://drive.google.com/file/d/0BxRUime4DPjvdGZjb1ZCOUFSNVU/view?usp=drive_web> 2016-03-17 11:40 GMT-04:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > 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) > > > > > > 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: > > using write iterations = 0 > > sampling 7 neighbors out to a distance of 12 mm > > reading patch > /home/jbang/Projects/replay/mri//replay06/surf/lh.oc.patch.3d > > with 30434 vertices (20.5% of total) > > MRISreadPatch: bad vertex # (148517) found in patch file > > No such file or directory > > > > When making the patch lh.oc.patch.3d, I followed the processes below: > > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino > > -contrast UpperLower > > > > 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.oc.patch.3d > > > > So I think I made the patch correctly. > > > > ! weird thing that I suspect is that when I click save patch as, the > default > > location is $SUBJECTS_DIR/fsaverage/surf/ , so I had to change it to > > $SUBJECTS_DIR/$SUBJECT/surf > > > > Could you please help me? > > > > Thanks a lot! > > > > 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. > >
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