Hi,
Sorry for the answer too late.
I tried the command to evaluate the RMS distance but I just get the difference
between the 2 surfaces in terms of faces and vertices.
But I would compare my 2 surfaces by calculating the euler characteristic (
vertices-edges+ faces) .
Thank you so much for your help!!!
Lucille
________________________________
De : Bruce Fischl <fis...@nmr.mgh.harvard.edu>
À : Michael Harms <mha...@conte.wustl.edu>
Cc : Lucille Deroche <lucilledero...@yahoo.fr>; Douglas N Greve
<gr...@nmr.mgh.harvard.edu>; "freesurfer@nmr.mgh.harvard.edu"
<freesurfer@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
>
> 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>
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> >
> >
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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> information in this e-mail is intended only for the person to whom it is
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