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Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
Hi André,
Could you send the command that you ran to produce this ouput? Also (just to
check), do you have permissions to read the b0_brain.nii.gz file, and is it
here:
/Applications/freesurfer/subj
urfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Lee Tirrell
[ltirr...@nmr.mgh.harvard.edu]
Gesendet: Freitag, 27. März 2015 19:07
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
On Thu, 26 Mar 2015, André Schmidt wrote:
Hi Andre,
Try using
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
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:
ard.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 fo
.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 fi
27;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 a2
]" 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
[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
-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&#
fer] 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
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
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 seed
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