Hi Anastasia,

On a related note, with tracula, you can't let's say track the amygdala to the vmpfc (there is a study already demostrating that there is a white matter tract that connects these two structures). Can I do something like that.......take the amygdala as the seed and the vmpfc as the target? Based on your response I am guessing no?

Thanks,

Emily

----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Monday, March 31, 2014 6:32:17 PM Subject: Re: [Freesurfer] SEEDING in Tracula

Hi Durai - Tracula is not for exploratory tractography, i.e., to answer questions like "what is this region connected to"? It uses prior anatomical information on known pathways to reconstruct those specific pathways. The anatomical information comes from the FreeSurfer anatomical segmentation of the same subject, and it's not just a seed region, but rather the probability of the pathway to go through each label in the anatomical segmentation at each point along the pathway's trajectory.

Hope this helps, a.y

On Sat, 29 Mar 2014, Durai Arasan wrote:

Hi Freesurfer experts, So I have seen studies where tracula was used to examine one of the 18 major tracts.

However can tracula perform seed based probabilistic tractography? i.e. can I seed ANY region and specify targets etc?

I guess I am asking if it can do LOCAL tractography of any kind?

Thank you!

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Hi Emily - I don't remember off the top of my head where this is mentioned, but it probably refers to the FA, MD, etc maps. An ROI-based analysis would be one where you average the FA in an ROI, so it doesn't refer to tractography.

Hope this helps, a.y

On Mon, 31 Mar 2014, ebelleau@uwm.edu wrote:

Hi Anastasia,

Although the website says: In addition to the tract-based analysis that can be performed on the tract-based averages of anisotropy and diffusivity, the same maps could also be used for other voxel-based and ROI-based group analyses.

So this makes me think that this type of group based ROI analysis is possible?

Emily ----- Original Message ----- From: ebelleau@uwm.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Monday, March 31, 2014 10:53:08 PM Subject: Re: [Freesurfer] SEEDING in Tracula

Hi Anastasia,

On a related note, with tracula, you can't let's say track the amygdala to the vmpfc (there is a study already demostrating that there is a white matter tract that connects these two structures). Can I do something like that.......take the amygdala as the seed and the vmpfc as the target? Based on your response I am guessing no?

Thanks,

Emily

----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Monday, March 31, 2014 6:32:17 PM Subject: Re: [Freesurfer] SEEDING in Tracula

Hi Durai - Tracula is not for exploratory tractography, i.e., to answer questions like "what is this region connected to"? It uses prior anatomical information on known pathways to reconstruct those specific pathways. The anatomical information comes from the FreeSurfer anatomical segmentation of the same subject, and it's not just a seed region, but rather the probability of the pathway to go through each label in the anatomical segmentation at each point along the pathway's trajectory.

Hope this helps, a.y

On Sat, 29 Mar 2014, Durai Arasan wrote:

...

Hi Freesurfer experts, So I have seen studies where tracula was used to examine one of the 18 major tracts.

However can tracula perform seed based probabilistic tractography? i.e. can I seed ANY region and specify targets etc?

I guess I am asking if it can do LOCAL tractography of any kind?

Thank you!

---

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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