ROI to ROI tractography

[Zachary Anderson]

Hello all!

I'm a relative new comer to the world of diffusion imaging so I hope this isn't too naive a question. I've really enjoyed working with AFQ so far. I've made it through the tutorials but have used some data from our lab and the images are striking. But I'm wondering how easy it is to constrain the fiber tracking procedure to only take tracts that connect two specific ROI's. For example, if I were interested specifically in tracts that connect the NAcc to the mOFC, is there an easy way to implement that in AFQ? I really appreciate the help!

Thanks,

Zach

[Jason Yeatman]

If you dive into the AFQ_AddNewFiberGroup function you could probably make that work. If you have ROIs to define a fiber group, it is easy to add it into AFQ

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[Zachary Anderson]

Excellent, thanks for the quick response! I appreciate the guidance, I'll be diving in soon.

On Tuesday, May 26, 2020 at 7:19:56 PM UTC-5, Jason wrote:

If you dive into the AFQ_AddNewFiberGroup function you could probably make that work. If you have ROIs to define a fiber group, it is easy to add it into AFQ

On Tue, May 26, 2020 at 3:51 PM Zachary Anderson <zacharyan...@u.northwestern.edu> wrote:

Hello all!

I'm a relative new comer to the world of diffusion imaging so I hope this isn't too naive a question. I've really enjoyed working with AFQ so far. I've made it through the tutorials but have used some data from our lab and the images are striking. But I'm wondering how easy it is to constrain the fiber tracking procedure to only take tracts that connect two specific ROI's. For example, if I were interested specifically in tracts that connect the NAcc to the mOFC, is there an easy way to implement that in AFQ? I really appreciate the help!

Thanks,

Zach

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[Zachary Anderson]

It all worked great! I had a quick follow up question. I noticed in the AddNewFiberGroup script that it transforms masks into an individuals space. A post doc in our lab used a specialized warping function to our data and so we were wondering if there was a way to circumvent the warping performed by the new fibers script. The idea would be to warp our ROI's using the function he has and then to run the AddNewFiberGroup script. Would this be an easy fix on our end or is there a better way to go about this?

On Tuesday, May 26, 2020 at 7:19:56 PM UTC-5, Jason wrote:

If you dive into the AFQ_AddNewFiberGroup function you could probably make that work. If you have ROIs to define a fiber group, it is easy to add it into AFQ

On Tue, May 26, 2020 at 3:51 PM Zachary Anderson <zacharyan...@u.northwestern.edu> wrote:

Hello all!

I'm a relative new comer to the world of diffusion imaging so I hope this isn't too naive a question. I've really enjoyed working with AFQ so far. I've made it through the tutorials but have used some data from our lab and the images are striking. But I'm wondering how easy it is to constrain the fiber tracking procedure to only take tracts that connect two specific ROI's. For example, if I were interested specifically in tracts that connect the NAcc to the mOFC, is there an easy way to implement that in AFQ? I really appreciate the help!

Thanks,

Zach

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[Jason Yeatman]

Yeah, you can either (a) switch your code in for the warping code or (b) warp the ROIs yourself and save them with the appropriate name in each individual's folder. At one point I switched to using ANTs for warping and you will see that there is a whole stream that let's you switch between ANTs or SPM. But AFQ looks for filenames and will use what's there if you save out your own ROIs

On Tue, Jun 2, 2020 at 6:54 PM Zachary Anderson <zacharyan...@u.northwestern.edu> wrote:

It all worked great! I had a quick follow up question. I noticed in the AddNewFiberGroup script that it transforms masks into an individuals space. A post doc in our lab used a specialized warping function to our data and so we were wondering if there was a way to circumvent the warping performed by the new fibers script. The idea would be to warp our ROI's using the function he has and then to run the AddNewFiberGroup script. Would this be an easy fix on our end or is there a better way to go about this?

On Tuesday, May 26, 2020 at 7:19:56 PM UTC-5, Jason wrote:

If you dive into the AFQ_AddNewFiberGroup function you could probably make that work. If you have ROIs to define a fiber group, it is easy to add it into AFQ

On Tue, May 26, 2020 at 3:51 PM Zachary Anderson <zacharyan...@u.northwestern.edu> wrote:

Hello all!

I'm a relative new comer to the world of diffusion imaging so I hope this isn't too naive a question. I've really enjoyed working with AFQ so far. I've made it through the tutorials but have used some data from our lab and the images are striking. But I'm wondering how easy it is to constrain the fiber tracking procedure to only take tracts that connect two specific ROI's. For example, if I were interested specifically in tracts that connect the NAcc to the mOFC, is there an easy way to implement that in AFQ? I really appreciate the help!

Thanks,

Zach

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