On Thu, 26 Mar 2015, André Schmidt wrote:
Hi Andre,
Try using the --seg flag with vol2label, as in:
mri_label2vol --seg left_putamen2.nii.gz --temp b0_brain.nii.gz --reg
registration2b0.dat --o left_putamen_dwi_seed
left_putamen2.nii.gz is a segmentation, where each voxel in the volume is
assigned a number (in your case 1 for left putamen and 0 everywhere else).
Freesurfer label files have a different format. Run mri_label2vol --help
for more information. Hope this helps, and let us know if there are more
problems.
Best,
Lee
Hi Anastasia,
Sorry for not being clearer.
According to your email, I have labelled all my regions of interest using this
command:
"mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o labelID.nii.gz"
Let's take the left putamen as an example:
"cmdline mri_binarize --match 12 --i aparc+aseg.mgz --o left_putamen2.nii.gz
sysname Darwin
hostname Andres-MacBook-Pro.local
machine x86_64
user andre
input aparc+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output left_putamen2.nii.gz
Binarizing based on matching values
nMatch 1
0 12
binval 1
binvalnot 0
Found 6228 values in range
Counting number of voxels
Found 6228 voxels in final mask
mri_binarize done"
Please find attached the output file (left_putamen2.nii.gz).
After this, I used the following command to create the register.dat file:
"bbregister --s HC001 --mov HC001/mri/bo_brain.nii.gz --reg
HC001/mri/registration2b0.dat --dti --init-fsl"
Please find attached the registration2b0.dat file.
Then I wanted to convert the label file into diffusion space with mri_label2vol
with this command:
"mri_label2vol --label left_putamen2.nii.gz --temp b0_brain.nii.gz --reg
registration2b0.dat --o left_putamen_dwi_seed
Number of labels: 1
left_putamen2.nii.gz
Annot File: (null)
Template Volume: b0_brain.nii.gz
Outut Volume: left_putamen_dwi_seed
Registration File: registration2b0.dat
Fill Threshold: 0
Label Vox Vol: 1
ProjType: (null)
ProjTypeId: 0
ProjStart: 0
ProjStop: 0
ProjDelta: 0.1
Subject: (null)
Hemi: (null)
UseNewASeg2Vol: 1
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: --------
-0.400 0.000 0.000 64.000;
-0.000 -0.000 -0.400 48.000;
-0.000 0.400 -0.000 27.000;
0.000 0.000 0.000 1.000;
Template Voxel Volume: 15.625
nHits Thresh: 0
Loading registration from registration2b0.dat
RegMat: --------
0.996 0.088 -0.024 3.909;
0.025 -0.007 1.000 0.627;
0.088 -0.996 -0.009 -10.557;
0.000 0.000 0.000 1.000;
Label RAS-to-Vox: --------
-0.398 -0.035 0.010 62.436;
-0.035 0.398 0.004 52.223;
0.010 -0.003 0.400 27.251;
0.000 0.000 0.000 1.000;
nlabels = 1
Allocating Hit Volume (663552) voxels
Loading left_putamen2.nii.gz
???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
mri_label2vol: could not scan # of lines from label file
ERROR reading left_putamen2.nii.gz"
Obviously something is wrong with the label file - do you see what I am doing
wrong?
Thank you
Andre
________________________________________
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Anastasia
Yendiki [ayend...@nmr.mgh.harvard.edu]
Gesendet: Dienstag, 17. März 2015 19:43
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
Hi Andre - There is no way for us to guess what went wrong if we don't
know the output of the command that you're trying to run. For example,
"something went wrong" could mean that that the command failed without
creating any volume, that the volume was created but it doesn't look
right, etc.
Please send us the command line that you type and all the text that the
command outputs on your terminal window.
a.y
On Tue, 17 Mar 2015, André Schmidt wrote:
Hi Anatasia,
I was able to create a registration.dat with bbregister now ("bbregister --s HC001
--mov HC001/mri/bo_brain.nii.gz --reg HC001/mri/registration2b0.dat --dti
--init-fsl"). However, I got an error message after using mri_label2vol - ERROR
reading left_accumbens.nii.gz
I think something went wrong with "mri_binarize --match ID --i aparc.a2009s+aseg.mgz
--o labelID.nii.gz"
For the left accumbens I used: "mri_binarize --match 12 --i aparc+aseg.mgz --o
left_putamen.nii.gz"
Sorry for this newbie question but I'm happy to get help
Cheers
Andre
_______________________________
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Anastasia
Yendiki [ayend...@nmr.mgh.harvard.edu]
Gesendet: Dienstag, 17. März 2015 16:59
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
Hi Andre - What do you mean by diffusion file? The registration file that
transforms between diffusion and anatomical space is output by bbregister
(see part A of the tutorial that I mentioned below).
a.y
On Tue, 17 Mar 2015, André Schmidt wrote:
Hi Anastasia,
I intend to use mri_label2vol to map the label file into the diffusion
space. Can you say me what for a diffusion file I can use for that and
where I can find it?
Thanks again for your help
Andre
________________________________________
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Anastasia
Yendiki [ayend...@nmr.mgh.harvard.edu]
Gesendet: Donnerstag, 26. Februar 2015 19:05
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
Hi Andre - I'd go through the multimodal integration tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview
a.y
On Thu, 26 Feb 2015, André Schmidt wrote:
Hi Anastasia,
Thank you very much for your help. I have created such a label nii file, for
example for ID 9, the left thalamus.
Can you please help me how I can map that file into diffusion space using
bbregister? I would like to use it then for probtrackx.
Many thanks again.
Andre
________________________________________
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Anastasia
Yendiki [ayend...@nmr.mgh.harvard.edu]
Gesendet: Donnerstag, 26. Februar 2015 16:09
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
Hi Andre - You find the ID number of each of the regions you're interested
in, from $FREESURFER_HOME/FreeSurferColorLUT.txt. Then you run:
mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o yourlabel.nii.gz
Then you'll have to map that label into DWI space. We recommend bbregister
for the cross-modal registration.
a.y
On Thu, 26 Feb 2015, André Schmidt wrote:
Dear freesurfer experts,
I intend to use the aparc.a2009s.annot file as seed regions for a tractography
analysis. I like to compute streamlines between every region
in the annot file. Can you please guide me how I can create masks for every
region in the annot file (or a text file with all seeds
including their paths)?
Many thanks for your help.
Andre
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