Tim,


In the currently released version if you use --seed= and --mask2= you get the usual symmetric output:

 

Log directory is: /T/Projects/DTI/WadaLanguageStudy/EP009RK1/data.StructuralColorMaps/Results/R_STG_to_IFG_Results

1_1

1_2

1_3

2_1

2_2

2_3

7

78 81 103

…

78 78 113

added

73 117 100

…

88 117 121

Finished

 

Peace,

 

Matt.

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Tim Behrens
Sent: Wednesday, June 11, 2008 8:48 AM
To: [log in to unmask]
Subject: Re: [FSL] ProbTrack - selecting threshold

 

you can't do 2 mask symmetric any more can you? You have to use multiple masks and waypoints, which will output waytotal.txt

 

T

 

On 11 Jun 2008, at 12:07, Matt Glasser wrote:



Tim,

 

I have noticed that file seems not to be made in 2 mask symmetric tractography.  Is that a bug, or by design?

 

Matt.

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Tim Behrens
Sent: Wednesday, June 11, 2008 1:19 AM
To: [log in to unmask]
Subject: Re: [FSL] ProbTrack - selecting threshold

 

Thanks Matt - completely agreed - just one thing to add. 

 

If you are using waypoint masks to define a tract, then sometimes your results may look more consistent across subjects if you threshold as a proportion of the total number of samples that made it between the 2 masks rather than the total number sent from the ROI. This number is stored in waytotal.txt.

 

T

 

On 11 Jun 2008, at 03:06, Matt Glasser wrote:




Since I was the one who decided on the threshold in the referenced paper, I might warn you that it was based on what worked well for those datasets to exclude low probability voxels that were not of interest while preserving higher probability voxels that were.  I just completed arcuate tractography on another dataset, and got a rather different threshold value that seemed to work best 2.0e-6 % of total samples sent out from the ROIs.  One difference between the two datasets is that my seed space in the below referenced paper was in diffusion space, whereas in the new study, it is in structural space.  Thus, if the DTI resolution were 2x2x2mm and the structural resolution were 1x1x1mm, each voxel of DTI space would correspond to 8 voxels of structural space, and this may be the cause of the difference.  Because probtrackx produces a continuous probability distribution, there is no “rule of thumb” that allows you to threshold results from any tract in any dataset at the same absolute number.  I think two things are important: 1) That you use a consistent percentage of the total number of samples sent out for each tract across subjects (so that tracts created by larger ROIs, and thus have more total samples sent out, have higher thresholds) and 2) That in setting the percentage that you will use, you try a variety of values and see what seems to produce clean results showing the pathway of interest without many extraneous pathways not clearly connected to the ROI but at the same time does not remove large parts of the pathway of interest (because it is too high).  Tim et al may have further thoughts.  You can reduce the amount of extraneous pathways by carefully choosing your method of tractography (i.e. the ROIs you use) and using the colors and lines displays of FSLView to get an understanding of what the diffusion is doing in your pathways of interest and/or restricting your pathways to white matter by segmenting a structural image and turning greymatter and CSF into a “stop” mask.  If you use fairly large ROIs and get pathways of few samples, that may suggest that any pathway between the regions is either very weak or does not exist.

 

Peace,

 

Matt.

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Ted Yanagihara
Sent: Tuesday, June 10, 2008 9:41 PM
To: [log in to unmask]
Subject: Re: [FSL] ProbTrack - selecting threshold

 

This is a great paper to start with. Be sure to read the supplementary material for more info on the methods.

 

Rilling et al. Nature Neuroscience (2008) vol. 11 (4) pp. 426-428

 

Hope it helps!

 

ted

 

On Jun 10, 2008, at 9:28 PM, Ruth Carper wrote:





Hi,

I'd like to use ProbTracks to identify some white matter tracks. Do you

have any suggestions for selecting a threshold value to define a tract?

i.e. I have seed and target masks which produce an intervening tract, but

many of the voxels have very low values (indicating few streamlines). How

do I select a good cutoff value for what I can be confident is the real

tract? Any rule of thumb?

 

--Ruth