Hi Laouchedi, I still cannot figure out why you are getting a volume of
all 0s. Are you sure it is all 0s and not that the label is so small it
is hard to find? Check again, and if it is all 0s for sure, send me the
commands you made to make the annotation and I'll see if I can replicate
it here.

doug


On 06/28/2013 01:45 PM, LAOUCHEDI MAKHLOUF wrote:
> excuse me Doug.
>
> i gathered previous correspondences (i wrote your replies are in bold) :
>
>
>
> june, 28 at 16:41
>
> 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
> june, 28 at 16:41
>
> *The terminal output, ie, what gets printed to the screen after your run
> the program.*
>
> june, 28 at 16:39
> excuse me but i don't understand what you mean by "terminal of
> mri_label2volume"
> Thank you for help
>
>
> june, 28 at 16:33
>
> *please post responses to the list
> doug
> btw, there is no terminal output below*
>
> june, 28 at 16:29
>
> i used tksurfer to display the volume and i imported the annotation
> file created, it looks ok. about the full terminal ouput of
> mri_label2vol :
> /home/mlaouche/lh.G_and_S_cingul-Ant.nii.gz  --proj frac 0 1 .1
> Thanks
>
> (in fact i used to assemble individual labels to make some annotation
> files for some parts of the brain, which i used to transform to nifti
> using mri_label2vol without problem)
> june, 28 at 16:49
>
> Doug
> *How does the annot look on the surface (ie, intksurfer)? What is the
> full terminal output of mri_label2vol? *
>
> june, 28 at 16:19
>
> 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
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
> *De :* Douglas N Greve <greve@nmr.mgh.harvard.edu>
> *À :* LAOUCHEDI MAKHLOUF <laoumakhl@yahoo.fr>
> *Envoyé le :* Vendredi 28 juin 2013 18h41
> *Objet :* Re: [Freesurfer] mri_label2vol problem
>
>
> 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
> <mailto:greve@nmr.mgh.harvard.edu>>
> > *À :* freesurfer@nmr.mgh.harvard.edu
> <mailto: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
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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> >
> > _______________________________________________
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> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to whom
> > it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
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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
>
> 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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>

--
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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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