Print

Print
Ok, thanks Saad, I misunderstood. And the waypoint condition should be AND, correct? Because I want tracking to go through the CC and ROI_2.

This method works well when the pathway from one ROI to another is known, but in my network this isn't always the case. Is there a way to for the tracking to occur just between the 2 ROIs?

Also, I ran probtrackx2 with the opposite ROIs. So ROI_1 (right preSMA) as a seed mask and ROI_2 (left preSMA) as a waypoint and termination mask. I got different results than my first analysis with ROI_1 = left preSMA and ROI_2 = right preSMA. In probtrackx2 under the options tab -> waypoint options, "Apply waypoint independently to both directions" is clicked. I thought this option meant that tracking goes from ROI_1 -> ROI_2 and ROI_2 -> ROI_1. Why would running the second analysis produce a different result than the first?

I thought that maybe differences in the second analysis could be due to the fact that there is a different termination mask in analysis 1 and 2. So in a 3rd analysis, I ran both analysis 1 and 2 (lets call them analysis 3.a and 3.b respectively) without a termination mask. Again, analysis 3.a and 3.b produced different results. Is this to be expected?



On Thu, Apr 18, 2013 at 11:28 AM, Saad Jbabdi <[log in to unmask]> wrote:
Hi - yes that was clear. Including the CC as a waypoint means that it will exclude tracts that do not go through the CC.

Cheers
Saad


On 18 Apr 2013, at 17:40, Dana Wagshal <[log in to unmask]> wrote:

Hi Saad,

Sorry if I wasn't clear. I want to keep the tracks that go through the CC but not other tracks that aren't biologically plausible. In my fdt_paths.nii.gz file, I see a circular path that crosses to the other hemisphere above the CC from the left preSMA to the right preSMA. These are the paths that I don't want. Maybe it would help if I attach my output files.

Please reference the attached files. My dti_FA.nii.gz file was too large so it's not in the attached files.

Best,
Dana


On Thu, Apr 18, 2013 at 2:27 AM, Saad Jbabdi <[log in to unmask]> wrote:
Hi Dana
If you want to exclude tracts that don't go through the CC, then you can add the CC as a waypoint mask (in addition to the target roi). 

Cheers,
Saad

On 17 Apr 2013, at 22:20, Dana Wagshal <[log in to unmask]> wrote:

Hi FSL group,

I want to complete tractography in an eye-movement network with 16 ROIs. I'm interested in the pairwise connections between each ROI pair (ex. ROI_1 -> ROI_2, ROI_1 -> ROI_3, etc) and obtaining a measure of FA as well as the trajectory between each ROI pair. So I started out with using ROI_1 (ex- left preSMA) as a seed mask and ROI_2 (ex- right preSMA) as a waypoint. When I did this there were tracks that went through the corpus callosum as expected. However, I noticed that there were tracks that went beyond the right preSMA and tracks that seemed to connect at the very top portion of the brain not using the corpus callosum. Since I didn't want it to extend past ROI_2 I also put ROI_2 as a termination mask. This seemed to solve that problem. However, there still seems to be a good number of tracks that connect the right and left preSMA that don't go through the corpus callosum but at a higher level of the brain, which doesn't seem anatomically possible.

1) Why is this happening?
2) Is there a way to stop this from occurring and to get a track that ONLY goes from ROI_1 to ROI_2 and vice versa?

Your help would be greatly appreciated!

Dana


--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)














--
-Dana
<rpreSMA_to_FA_bin.nii.gz><lpreSMA_to_FA_bin.nii.gz><fdt_paths.nii.gz>

--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)














--
-Dana