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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