HiLucille, you can use mris_diff with the --xyz-rms optionto compute the RMS difference. Don't know about Hausdorff doug
On 04/12/2013 09:39 AM, Lucille Deroche wrote: > Hi , > > Thank you so much for the answer Bruce and Michael. > I tried the command given by Michael and it works. > I didn't already find a way for calculating the RMS distance between > matched vertices and Hausdorff. > As soon as I do that, I will compare the results and I'll give you a > feedback. > > Cheers > Lucille > > ------------------------------------------------------------------------ > *De :* Bruce Fischl <fis...@nmr.mgh.harvard.edu> > *À :* Michael Harms <mha...@conte.wustl.edu> > *Cc :* Lucille Deroche <lucilledero...@yahoo.fr>; > "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>; > Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *Envoyé le :* Jeudi 11 avril 2013 16h02 > *Objet :* Re: [Freesurfer] Autoreg-sess and mri_surf2vol > > yes, I agree. Two surfaces could be extremely close and have 0 dice. I > don't think it would be as informative as Hausdorff or RMS as Mike > suggests > > Bruce > On Thu, 11 Apr 2013, Michael Harms wrote: > > > > > Try: > > mri_surf2vol --surf pial --mkmask --hemi lh --identity <subjid> > --template <subjid>/mri/norm.mgz --o > > <subjid>/mri/pial_in_vol.mgz > > > > FWIW, I'm not sure if sampling two surfaces to the volume, and then > computing a dice coefficient is > > really the best way to "compare" two surfaces. I would instead > compare the two surfaces directly -- > > e.g., the rms distance between matched vertices. > > > > cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Conte Center for the Neuroscience of Mental Disorders > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu <mailto:mha...@wustl.edu> > > > > From: Lucille Deroche <lucilledero...@yahoo.fr > <mailto:lucilledero...@yahoo.fr>> > > Reply-To: Lucille Deroche <lucilledero...@yahoo.fr > <mailto:lucilledero...@yahoo.fr>> > > Date: Thursday, April 11, 2013 2:39 PM > > To: Doug Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>, "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Subject: Re: [Freesurfer] Autoreg-sess and mri_surf2vol > > > > Hi, > > > > I did the command: > > mri_surf2vol --surfval $SUBJECTS_DIR/Patient1/surf/rh.pial --hemi rh > --identity Patient1. > > ERROR: cannot recognize the type of > > /home/lucille/Freesurfer/freesurfer/subjects/Patient1/surf/rh.pial > > The name of my subject is ' Patient1'. > > Did I do a wrong entery at the --surfval argument ? > > > > > > Cheers > > Lucille > > > > > _____________________________________________________________________________________________________ > > De : Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > À : freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > Envoyé le : Jeudi 11 avril 2013 12h49 > > Objet : Re: [Freesurfer] Autoreg-sess and mri_surf2vol > > > > > > Hi Lucile, don't use autoreg-sess (that is an old program and was for > > fMRI). Use mri_surf2vol with --identity subjectname instead of --reg > > doug > > > > On 04/11/2013 11:45 AM, Lucille Deroche wrote: > > > Hi Bruce, > > > > > > In fact, have 2 differents surfaces of pial surface. I would like > > > to save my surfaces in volume to be able to calculate the dice score > > > between the two. > > > > > > Cheers > > > > > > Lucille > > > > ------------------------------------------------------------------------ > > > *De :* Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > > > *À :* Lucille Deroche <lucilledero...@yahoo.fr > <mailto:lucilledero...@yahoo.fr>> > > > *Cc :* "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > *Envoyé le :* Jeudi 11 avril 2013 11h18 > > > *Objet :* Re: [Freesurfer] Autoreg-sess and mri_surf2vol > > > > > > Hi Lucille > > > > > > what do you mean by converting a surface to the volume? What do > you want > > > to do with it? What volume would you like to convert it to? > > > > > > cheers > > > Bruce > > > On Thu, 11 Apr > > > 2013, Lucille Deroche wrote: > > > > > > > Hi, > > > > My name is Lucille and I'm really new with Freesurfer : My > > > questions are very basic, sorry. > > > > I just start a project in segmentation of cerebrum. > > > > For converting a surface in volume. I would like to use > > > mri_surf2vol but for that I need a > > > > volume registration file . For creating that file, I would use > > > autoreg-sess. > > > > In documentation, it is said that : 'The volume registration file > > > contains the matrix that > > > > maps XYZ in the reference anatomical to XYZ in the functional > volume' > > > > My question is : what here, represent the anatomical reference ? The > > > functionnal volume ? > > > > Secondly, for autoreg-sess, the arguments are the subject name and > > > the subject directory. I > > > > think the registration I need to create must be between my 2 > > > volumes, so should I use the > > > > subject name and subject directory for my 2 subjects ? > > > > > > > > Sorry,I am really messed... > > > > > > > > Cheers > > > > Lucille > > > > > > > > > > > _______________________________________________ > > > 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>> > > > 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 <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> > > 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 > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto: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. > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
