Print

---

Hi Matteo,

My 264 seeds were defined in standard space so when I ran probtrackx, I did
the standard2diff conversion. But yes, all the values off of the diagonal
are zero or very low.

I am attaching the log file to show my exact command. It is -omatrix1 which
should generate seed by seed connectivity.

Thank you for your help!
Levi

set tool probtrackx

set probtrack(usereference_yn) 1

set probtrack(xfm)
/mnt/engram/projects/~/data/~/038/Diffusion/data.bedpostX/xfms/standard2diff.mat

set probtrack(bedpost_dir)
/mnt/engram/projects/~/data/leviDiff/038/Diffusion/data.bedpostX

set probtrack(xfm)
/mnt/engram/projects/~/data/leviDiff/038/Diffusion/data.bedpostX/xfms/standard2diff.mat

set probtrack(mode) network

set probtrack(exclude_yn) 0

set probtrack(usereference_yn) 1

set probtrack(verbose_yn) 0

set probtrack(loopcheck_yn) 1

set probtrack(modeuler_yn) 0

set probtrack(curvature) 0.2

set probtrack(nsteps) 2000

set probtrack(steplength) 0.5

set probtrack(nparticles) 5000

set probtrack(fibthresh) 0.01

set probtrack(distthresh) 0.0

set probtrack(sampvox) 0.0

set probtrack(oneway_yn) 1

set probtrack(wayorder_yn) 0

set probtrack(waycond) AND



On Sun, Jul 12, 2015 at 2:35 PM, Matteo Bastiani <
[log in to unmask]> wrote:

> Hi Levi,
>
> can you please tell me which exact command you ran to obtain your
> structural connectome?
>
> Do you mean that all entries off of the diagonal are equal to zero or are
> very low? Did you define your seed voxels in native diffusion space?
>
>
> Cheers,
> Matteo
>
> > On 12 Jul 2015, at 18:23, Levi Solomyak <[log in to unmask]>
> wrote:
> >
> > Dear FSL Experts,
> >
> > I've been working on generating a structural connectivity matrix using
> diffusion data. To do so, I've been first creating 264 seed points
> (spherical roi's of radius 5) based on Powers et. al 2011 parcellation
> scheme, and then running probtrackx on the multiple masks condition (no
> termination, exclusion, or waypoint conditions) with -omatrix1 (seed by
> seed connectivity)  and with standard parameters.
> > This gives me a 264 by 264 whole brain structural connectivity matrix
> (once I average over the voxel). When I looked however,  only local
> projections were uncovered, and basically nothing off of the diagonal (in
> the fdt_network_matrix) showed anything.
> >
> > Does anyone have any suggestion for identifying where I went wrong or on
> how to generate the structural connectivity matrix that will actually
> identify projections?
> >
> > Thank you for your help!
> > Levi Solomyak
>