Hi Laouchedi, I have asked you two times now to include all previous
correspondences in each email. This is the 3rd time. If you are going to
make it hard for us to answer your question, then the result will be
that they won't be answered.
thanks
doug


On 06/28/2013 12:12 PM, LAOUCHEDI MAKHLOUF wrote:
> 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
> >
> >
> > _______________________________________________
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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