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
>>>
>>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
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>
>
>
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