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(a)nmr.mgh.harvard.edu>
À : LAOUCHEDI MAKHLOUF <laoumakhl(a)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(a)nmr.mgh.harvard.edu>
> *À :* freesurfer(a)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(a)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(a)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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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve(a)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/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
