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
> >
> >
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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
addressed. If you believe
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information, please contact the
Partners Compliance HelpLine at http://www.partners.org/complianceline . If the
e-mail was sent to
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