mri_mc uses marching cubes to build a tessellation, which mri_tesselate puts vertices on the corners of every voxel face that is a border between "on" and "off" voxels
cheers Bruce On Wed, 30 Nov 2011, Douglas N Greve wrote: > Hi Jie, what do you mean they don't work? I don't know what the > difference between mri_mc and mri_tesselate is (another good reason to > post to the list so that others who might know can answer the question). > doug > > Jie Shi wrote: >> Sorry I have forgot to describe our surface format. >> >> Vertex 1 x1 y1 z1 >> Vertex 2 x2 y2 z2 >> . >> . >> . >> Vertex n xn yn zn >> Face 1 v1 v2 v3 >> . >> . >> . >> >> >> On Tue, Nov 29, 2011 at 5:10 PM, Jie Shi <jie....@asu.edu >> <mailto:jie....@asu.edu>> wrote: >> >> Hi, thanks for your previous help, but I have more questions to >> bother you. I have tried mri_tesselete and converted the resulting >> surfaces into ascii format. These surfaces work in Matlab but in >> our mesh format like the following they don't. If I tesselate the >> surface by command mri_mc, the surfaces work in our format. So >> what is the difference between mri_tesselate and mri_mc? Since the >> resulting surfaces are not good enough (some of them have holes), >> I would line to know if FreeSurfer can generate surfaces for >> subcortical structures like it does for cortex? Thanks a lot. >> >> Jie >> >> >> >> On Wed, Nov 9, 2011 at 5:24 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> yes, that has the subcortical segmentation based on the >> automatic algorithm and any changes that you might have made >> manually. The "auto" is only the result from the automatic method. >> doug >> >> Jie Shi wrote: >> >> Thanks a lot. Will try. Basically, is aseg.mgz the >> resulting file which contains the results of FreeSurfer >> subcortical segmentation? What role is the aseg.auto.mgz? >> >> Jie >> >> >> On Wed, Nov 9, 2011 at 5:15 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >> cd $SUBJECTS_DIR/subject/surf >> mri_tesselate ../mri/aseg.mgz 17 lh.hippocampus; # this >> generates >> a surface with jagged edges >> mris_smooth -nw -n 10 lh.hippocampus lh.hippocampus.sm10; # >> smooths surface 10 smoothing steps is just a guess >> >> # Visusalize the surface >> tksurfer subject lh hippocampus.sm10 >> # See the surface overlaid on the volume >> tkmedit subject orig.mgz lh.hippocampus.sm10 -aseg >> >> Not that when you run the tkmedit/tksurfer commands, >> they will >> complain that the surface does not match. This is not a >> problem >> for this application. >> >> doug >> >> >> Jie Shi wrote: >> >> Hi, thank you very much. Actually we do want to >> know how to >> get the surfaces in order to compare with ours. >> >> Jie >> >> >> On Wed, Nov 9, 2011 at 4:59 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: >> >> You can extract a binary mask for any structure with >> mri_binarize --i aseg.mgz --match XX --o >> yourmask.mgh >> where XX is a number from >> $FREESURFER_HOME/FreeSurferColorLUT.txt >> (eg, 17 = left hippo) >> It is possible to generate hippo surfaces, but >> we cannot >> guarantee >> accuracy. Let me know if you want to know how. >> doug >> >> Jie Shi wrote: >> >> Hi, experts. We need to use FreeSurfer to >> process some >> analyze >> image data. More specifically, we want to >> extract the >> hippocampus surfaces. We know that >> FreeSurfer has done >> subcortical segmentation during -autorecon2 >> stage in >> recon-all. We have checked the resulting >> aseg.mgz file and >> found that it contains all substructures. So >> we wonder if >> there is a way to get the separated .mgz >> files for each >> substructure or could FreeSurfer generate >> the subcortical >> surfaces? Thanks a lot. >> >> Best, >> Jie >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> <tel:617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>>> Fax: 617-726-7422 >> <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> <tel:617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>>> >> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> >> 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. >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 >> <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: >> 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
