That should work for 2-mask symmetric mode.  I am not familiar with network
mode, so I'll leave that to Tim or Saad.

Peace,

Matt.

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of John D. Griffiths
Sent: Wednesday, August 13, 2008 3:41 AM
To: [log in to unmask]
Subject: Re: [FSL] ProbTrack - selecting threshold

Hi Tim+Matt+Ruth+all

Sorry to butt in - but could I just if you could clarify what was meant
here: 

The following was written on behalf of Tim 

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

...which was in response to Matt's observation

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

Does this mean that to get a waytotal number for thresholding probtrackx
outputs generated in 2-mask symmetric mode (or --network mode with two
masks) that I need to re-run the analysis specifying one of the masks as a
seed and one as a waypoint? Would I also need to do vice versa and sum the
two?


Cheers,
            John




On Wed, 11 Jun 2008 16:42:29 -0400, Matt Glasser <[log in to unmask]> wrote:

>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
>
>http://www.nature.com/neuro/journal/v11/n4/abs/nn2072.html
>
>
>
>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
>
>
>
>
>
>
>
>