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
From: Lucille Deroche lucillederoche@yahoo.fr Reply-To: Lucille Deroche lucillederoche@yahoo.fr Date: Thursday, April 11, 2013 2:39 PM To: Doug Greve greve@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 greve@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 fischl@nmr.mgh.harvard.edu *À :* Lucille Deroche lucillederoche@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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