Hi Daniel - TRACULA uses manually labeled examples of tracts to learn from. That template simply defines the coordinate space in which those training examples live. If you were to provide a different set of manually labeled tracts that lived in a different space, that's when you'd provide a different template volume to specify what that space is. Changing the template volume without changing the manually labeled tracts that are used for training TRACULA wouldn't work.

a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daniel Callow <ddcc2442@gmail.com>
Sent: Monday, July 29, 2019 6:58:16 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA for kids/children
 

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Thank you for your response. We may have some children slightly younger so I am not sure if the method would still apply. Does that mean my suggested edit of changing the mni template to a different template wouldn’t work. I appreciate your input and quick response!

Kind regards,
Daniel Callow

On Mon, Jul 29, 2019 at 6:43 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:
Hi Daniel - What is the age range you're interested in? We have used tracula with children as young as 5 (see example ref below). Keep in mind that tracula is not a traditional template-based approach that needs perfect alignment to a template, because it finds tracts based on their relative position with respect to the labels in the individual aparc+aseg, rather than their absolute coordinates in some template space.

https://www.ncbi.nlm.nih.gov/m/pubmed/24269273/

For neonates, we have a new training set of manually labeled tracts in neonates that can be used by tracula. That option, however is not yet in the official freesurfer release.

https://www.ncbi.nlm.nih.gov/m/pubmed/31132451/

a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daniel Callow <ddcc2442@gmail.com>
Sent: Monday, July 29, 2019 6:31:37 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA for kids/children
 

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Hello, 

Is it possible to run TRACULA on baby/children brain scans? If so how would one go about doing this? 

Could I just change 

set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

to a different baby/child atlas? If not how would I go about this?

Best,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
443-254-6298
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Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2442@gmail.com
443-254-6298