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FSL  November 2018

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Subject:

Re: probtrackx 2 masks as seed space vs 1 seed mask + 1 waypoint mask

From:

Saad Jbabdi <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 8 Nov 2018 14:28:26 +0000

Content-Type:

text/plain

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Hi Max

The multi-mask option in your case simply runs sequentially two tractographies where first the seed is one of the masks and the waypoint is the other, then it swaps the seed and waypoint masks and runs a second time and adds the two fdt_paths.  Because generally seeding from one mask or the other does not necessarily produce the exact same pathways, this may explain why the two seed approach gives you a thicker looking tract.

Best wishes
Saad


> On 7 Nov 2018, at 09:25, Maximilian Jung-Botho <[log in to unmask]> wrote:
> 
> Dear FSL community,
> 
> I'm extremely new to all of this so I'm really sorry if this question is stupid. I'm just now learning the ropes of working with FSL and probtrackx in particular. I'm trying to find the Arcuate fasciculus through probabilistic fiber tracking.
> 
> I'm currently trying an approach were you define 2 ROIs, one in the posterior region of the inferior frontal gyrus and one in the posterior region of the superior temporal gyrus. What I've noticed is that when I set both ROIs as seeds (i.e. multiple masks as seed space), it'll produce a fiber bundle that is much thicker as when I set one ROI as a seed and the other as a waypoint mask. So far, I don't really understand why that is. From what I've learned from the FslWiki, the option of multiple masks as seeds will start the tracking algorithm from all seed masks and then retain only the fibers that pass through at least on other mask besides the one it originated from. So, in my particular case, the algorithm would start from both seeds and then only retain fibers that passed through the other one, respectively.
> 
> However, with a single seed mask and one waypoint mask, the algorithm only starts from the seed and then only fibers are retained that pass through the waypoint.
> 
> But if, in both cases, only fibers are retained that pass through both ROIs, shouldn't I get a similar result? Why does the 2 seed mask approach create a much thicker fiber bundle?
> I thought maybe it was because since the algorithm starts from both ROIs, it might be because the program basically works with double the amount of samples. But when I doubled the number of samples used for the 1 seed + 1 waypoint approach, the fiber bundle was still much thinner than the one created with 2 seed masks.
> 
> Can someone help me understand why that is? It would make sense to me if I were using a lot of masks but with only two, what's the difference between two seeds and one seed and a waypoint that produces vastly different results?
> 
> Again, I'm sorry if this is something very obvious that I'm just not getting. I'm really just starting out getting to know fiber tracking (and neuroimaging as a whole). In general, if anybody has any tips or recommendations what I should look up or work through to reliably find the Arcuate fasciculus, it'd be greatly appreciated!
> 
> Kind regards
> Max
> 
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