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 From: Lucille Deroche <lucilledero...@yahoo.fr> Reply-To: Lucille Deroche <lucilledero...@yahoo.fr> Date: Thursday, April 11, 2013 2:39 PM To: Doug Greve <gr...@nmr.mgh.harvard.edu>, "freesurfer@nmr.mgh.harvard.edu" <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> À : 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> > *À :* Lucille Deroche <lucilledero...@yahoo.fr> > *Cc :* "freesurfer@nmr.mgh.harvard.edu" <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> > 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 -- 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 _______________________________________________ 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 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.
