External Email - Use Caution
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 *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
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
External Email - Use Caution
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 ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298
External Email - Use Caution
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
External Email - Use CautionHello,
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 *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
External Email - Use Caution
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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daniel Callow <ddcc2442@gmail.commailto:ddcc2442@gmail.com> Sent: Monday, July 29, 2019 6:31:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] TRACULA for kids/children
External Email - Use Caution
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 ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298
freesurfer@nmr.mgh.harvard.edu
-
Daniel Callow -
Yendiki, Anastasia