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> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
