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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