I just sum the pathways and the waytotal numbers; it is not an average it is
a sum.
You will have better alignment between your diffusion and structural images
if you unwarp the EPI. This is always the case as even at 1.5T there is
some distortion of the EPI. If you don't have a field map and don't care as
much about registration between your diffusion and structural images (but
care more about registration between your diffusion image and standard
space), you could register the FA to the FA template included with FSL using
first FLIRT with 12 DOF and then FNIRT. If diffusion to structural
alignment is important for what you are doing I would do it as I suggested
in that thread.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Vanessa Lim
Sent: Monday, September 14, 2009 1:30 PM
To: [log in to unmask]
Subject: Re: [FSL] averaging prob tracks DTI
Thanks Matt,
Yes, we are trying to track the callosal pathways between the A1s. Do you
average the tracks as well? i.e. In fslmaths -add then -div by 2? Or do
you just do the add for summing?
I used the standard registration in FDT but we thought about doing nfirt to
register the DTI, I've been reading the T1 to b-zero thread and averaging
pathways and another thread on averaging the tracks where I think you
suggested "unwarp your dti data (using a filedmap), then use FLIRT to
register them to the T1 (6DF) and use FNIRT to warp the subjects T1 to MNI
space and finally apply this whole transformation to your paths." but I
wasn't sure if we should do this when the registration seemed fine?
Thanks,
Vanessa
On 9/14/09 1:03 PM, "Matt Glasser" <[log in to unmask]> wrote:
> I am unclear on which pathways you are attempting to find. Are you trying
> to track callosal pathways between primary auditory cortices in both
> hemispheres? It is certainly likely when using a local tractography
method
> like that in probtrackx that you will not necessarily get exactly the same
> results when tracking in one direction vs another. If you want to get the
> common tracts in both methods, you could multiply the two results together
> (this is perhaps not exactly what you want, but it will enhance common
> pathways relative to noncommon pathways). If you just want to get all of
> the pathways, you can sum the two results. I would not say that you can
> assume that pathways found with one direction but not the other are
> necessarily wrong or invalid, though they may be less likely to be correct
> than pathways found with both directions. In my own work, I tend to track
> in both directions and then sum the results.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Vanessa Lim
> Sent: Monday, September 14, 2009 9:36 AM
> To: [log in to unmask]
> Subject: [FSL] averaging prob tracks DTI
>
> Hi,
>
> I have a left and right primary auditory cortex (A1) masks which I used as
> seeds going
> from for example: mask image Left A1 and using the waypoint mask of the
> right A1 and I
> did the same analyses on the same Ss but reversing the left and right
mask,
> with the left
> A1 now the waypoint mask.
>
> I get different tracks for LA1 to RA1 compared RA1 to LA1 for all the
> subjects. Is this
> correct? If so, is it valid to try and get only the tracks that are
common
> to both left to right
> and right to left? If it is valid, can anyone please tell me how I might
> accomplish this
> please?
>
> Many thanks,
> Vanessa
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