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 *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 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 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/
Freesurfer mailing list 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 HelpLine at http://www.partners.org/complianceline http://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 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/
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
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 HelpLine at http://www.partners.org/complianceline
http://www.partners.org/complianceline
http://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- 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/
Hi here are the commands i used to : 1) make my labels : mri_annotation2label --annotation aparc.a2009s --hemi rh --subject ctr1 --surf pial --outdir /home/mlaouche/makh_free/labels/ctr1
2) make the annotation files from the obtained labels : mris_label2annot --ctab /coconut/applis/src/freesurfer/FreeSurferColorLUT.txt --l /home/mlaouche/etude_finale/labels/ctr1/lh.G_and_S_cingul-Ant.label --subject ctr1 --a G_and_S_cingul-Ant --h lh 3)make my nifti volumes from annot files : mri_label2vol --annot lh.G_and_S_cingul-Ant.annot --temp /home/mlaouche/makh_free/ctr1/mri/brain.mgz --subject ctr1 --hemi lh --identity --fillthresh .5 --o /home/mlaouche/etude_finale/gyri_sulci/ctr1/lh.G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1
________________________________ De : Douglas N Greve greve@nmr.mgh.harvard.edu À : LAOUCHEDI MAKHLOUF laoumakhl@yahoo.fr Cc : "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Envoyé le : Vendredi 28 juin 2013 21h23 Objet : Re: [Freesurfer] mri_label2vol problem
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
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LAOUCHEDI MAKHLOUF