I don't think there is one between surfaces - you would need to compute it yourself. Pretty easy in matlab, although probably very slow On Fri, 12 Apr 2013, Douglas N Greve wrote:
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 fischl@nmr.mgh.harvard.edu *À :* Michael Harms mharms@conte.wustl.edu *Cc :* Lucille Deroche lucillederoche@yahoo.fr; "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu; Douglas N Greve greve@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: mharms@wustl.edu mailto:mharms@wustl.edu
From: Lucille Deroche <lucillederoche@yahoo.fr
mailto:lucillederoche@yahoo.fr>
Reply-To: Lucille Deroche <lucillederoche@yahoo.fr
mailto:lucillederoche@yahoo.fr>
Date: Thursday, April 11, 2013 2:39 PM To: Doug Greve <greve@nmr.mgh.harvard.edu
mailto:greve@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 <greve@nmr.mgh.harvard.edu
mailto:greve@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 <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
*À :* Lucille Deroche <lucillederoche@yahoo.fr
mailto:lucillederoche@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
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