here is the command and it's terminal :

mri_label2vol --annot G_and_S_cingul-Ant.annot --temp /home/mlaouche/makh_free/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity --fillthresh 0 --o /home/mlaouche/G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1

Number of labels: 0
Annot File:      G_and_S_cingul-Ant.annot
Template Volume: /home/mlaouche/makh_free/ctr2/mri/brain.mgz
Outut Volume: /home/mlaouche/G_and_S_cingul-Ant.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol: 1
ProjType:       frac
ProjTypeId:     2
ProjStart:      0
ProjStop:       1
ProjDelta:      0.1
Subject: ctr2
Hemi:     lh
UseNewASeg2Vol: 1
DoLabelStatVol 0
$Id: mri_label2vol.c,v 1.34.2.1 2011/03/22 18:09:04 greve Exp $
Template RAS-to-Vox: --------
-1.000   0.000   0.000   128.000;
-0.000 -0.000 -1.000   128.000;
-0.000   1.000 -0.000   128.000;
0.000   0.000   0.000   1.000;
Template Voxel Volume: 1
nHits Thresh: 0
Using Identity Matrix
RegMat: --------
1.000   0.000   0.000   0.000;
0.000   1.000   0.000   0.000;
0.000   0.000   1.000   0.000;
0.000   0.000   0.000   1.000;
Label RAS-to-Vox: --------
-1.000   0.000   0.000   128.000;
0.000   0.000 -1.000   128.000;
0.000   1.000   0.000   128.000;
0.000   0.000   0.000   1.000;
INFO: loading surface /home/mlaouche/makh_free/ctr2/surf/lh.white
nvertices = 138786
Reading thickness /home/mlaouche/makh_free/ctr2/surf/lh.thickness
Loading annotations from G_and_S_cingul-Ant.annot
reading colortable from annotation file...
colortable with 14176 entries read (originally /home_cluster/amesse/software/freesurfer5.1/FreeSurferColorLUT.txt)
annotidmax = 1
Allocating Hit Volume (16777216) voxels
nlabels = 1

PVF (null)
Thesholding hit volume.
done

De : Douglas N Greve <greve@nmr.mgh.harvard.edu>
À : freesurfer@nmr.mgh.harvard.edu
Envoyé le : Vendredi 28 juin 2013 16h49
Objet : Re: [Freesurfer] mri_label2vol problem

How does the annot look on the surface (ie, intksurfer)? What is the
full terminal output of mri_label2vol?

On 06/28/2013 10:19 AM, LAOUCHEDI MAKHLOUF wrote:
> Hi
> i run mri_label2annot to get individual annot files for all
> labels, then i run mri_label2vol to get nifti volumes of my labels
> using the following command :
> mri_label2vol --annot lh.G_and_S_cingul-Ant.annot --temp
> SUBJ_DIR/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity
> --fillthresh .5 --o ~/lh.G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1
>
> but the result is a volume with zero values (i changed --fillthresh .5
> to --fillthresh 0 and i got the same probleme)
>
> Thanks
>
>
> _______________________________________________
> 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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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