Hi all!
I'm very new using FS and I have some questions. I have been doing parcellations with the FreeSurferLUT on a few subjects, with the comand recon-all and it worked OK. Now I'd want to try with the AAL atlas, I mean, I want my subject's brain parcellated in the AAL atlas. I have the template corresponding to AAL parcellation in nifti format, so how can I obtain this parcellation in my subject space? what (and how) comands I have to use?
Thanks in advanced!
Cheers.-
Stella
We don't support the AAL atlas. The AAL atlas is just an atlas mapped through the volume transform into the individual subject's space. It does not take into account any landmarks and will be only approximate at best. If that is what you really want to do, I would suggest posting to the list of another software package that uses AAL (SPM?).
On 11/09/2016 05:07 PM, stella maris sanchez wrote:
Hi all!
I'm very new using FS and I have some questions. I have been doing parcellations with the FreeSurferLUT on a few subjects, with the comand recon-all and it worked OK. Now I'd want to try with the AAL atlas, I mean, I want my subject's brain parcellated in the AAL atlas. I have the template corresponding to AAL parcellation in nifti format, so how can I obtain this parcellation in my subject space? what (and how) comands I have to use?
Thanks in advanced!
Cheers.-
Stella
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, thanks for your response.
I have one question more. I was reading the mail archive and I found a few messages that talk about the mri_label2vol, vol2surf and surf2surf commands. Specially the first one (mri_label2vol) the user said that with it he moved the AAL to the subject's space. Do you think doing it can help me? I'm not sure about the inputs of the command. Stella
Yes, mri_label2vol is the right command for this
On 11/11/2016 12:20 PM, stella maris sanchez wrote:
Hi Doug, thanks for your response.
I have one question more. I was reading the mail archive and I found a few messages that talk about the mri_label2vol, vol2surf and surf2surf commands. Specially the first one (mri_label2vol) the user said that with it he moved the AAL to the subject's space. Do you think doing it can help me? I'm not sure about the inputs of the command. Stella
-- Sánchez, Stella M.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
stella maris sanchez