Re: [HCP-Users] connectome for monkeys // fiber trajectories

[Glasser, Matthew]

The main current limitation with the probabilistic trajectory feature (which 
tracks exactly which fiber is chosen by the tractography algorithm out of the 
1-3 modeled fibers in each voxel) is that it only works with single threaded 
probtrackx2, and not with the GPU accelerated version.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Coalson mailto:tsc...@mst.edu>>
Date: Thursday, April 11, 2019 at 1:41 PM
To: DE CASTRO Vanessa 
mailto:vanessa.decas...@cnrs.fr>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] connectome for monkeys // fiber trajectories

Connectome workbench is agnostic to species, though there are some defaults 
(identification symbol size) which default to a size suited to the human brain. 
 We frequently use it with primate data.

Workbench can display probabilistic trajectories generated with fsl's 
bedpostx/probtrackx tools (for the specific type of output that saves the fiber 
orientations used per-seed and per-voxel, matrix4 I think), but I don't think 
we have made a tutorial for it (and it still has some rough edges, as it hasn't 
been a priority for us).  The wb_command -convert-matrix4-to-workbench-sparse 
and -convert-fiber-orientations (or -estimate-fiber-binghams for starting with 
just the direction samples, but is less accurate) commands are the starting 
points - once you have converted the files to workbench formats with the 
expected extensions (currently .trajTEMP.wbsparse and .fiberTEMP.nii), loaded 
them into wb_view, enabled them in features or layers (I don't recall exactly 
how), clicking on a seed point will display the trajectories to/from it.

There is also wb_command -probtrackx-dot-convert, which allows converting the 
other probtrackx matrix types to cifti files (can show how much each 
voxel/vertex is used for a seed, but can't be displayed the way the trajectory 
files can).

Tim


On Thu, Apr 11, 2019 at 9:23 AM DE CASTRO Vanessa 
mailto:vanessa.decas...@cnrs.fr>> wrote:
Hi! I've started to work with the human connectome workbench, and I was 
wondering if is ready to use with monkeys as well, like Caret.

And I also read in the tutorial that you are already working in a new feature: 
probabilistic fiber trajectories... how soon it will come?? :D

Thank you very much for everything.

Sinceresly yours,

--

Vanessa DeCastro, PhD

Centre de Recherche Cerveau et Cognition - UMR 5549 - CNRS
Pavillon Baudot CHU Purpan
31052 Toulouse Cedex 03, France


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Re: [HCP-Users] connectome for monkeys // fiber trajectories

[Timothy Coalson]

Connectome workbench is agnostic to species, though there are some defaults
(identification symbol size) which default to a size suited to the human
brain.  We frequently use it with primate data.

Workbench can display probabilistic trajectories generated with fsl's
bedpostx/probtrackx tools (for the specific type of output that saves the
fiber orientations used per-seed and per-voxel, matrix4 I think), but I
don't think we have made a tutorial for it (and it still has some rough
edges, as it hasn't been a priority for us).  The wb_command
-convert-matrix4-to-workbench-sparse and -convert-fiber-orientations (or
-estimate-fiber-binghams for starting with just the direction samples, but
is less accurate) commands are the starting points - once you have
converted the files to workbench formats with the expected extensions
(currently .trajTEMP.wbsparse and .fiberTEMP.nii), loaded them into
wb_view, enabled them in features or layers (I don't recall exactly how),
clicking on a seed point will display the trajectories to/from it.

There is also wb_command -probtrackx-dot-convert, which allows converting
the other probtrackx matrix types to cifti files (can show how much each
voxel/vertex is used for a seed, but can't be displayed the way the
trajectory files can).

Tim


On Thu, Apr 11, 2019 at 9:23 AM DE CASTRO Vanessa 
wrote:

> Hi! I've started to work with the human connectome workbench, and I was
> wondering if is ready to use with monkeys as well, like Caret.
>
> And I also read in the tutorial that you are already working in a new
> feature: probabilistic fiber trajectories... how soon it will come?? :D
>
> Thank you very much for everything.
>
> Sinceresly yours,
>
> *--*
>
> *Vanessa DeCastro, PhD*
>
> *Centre de Recherche Cerveau et Cognition - UMR 5549 - CNRS
> Pavillon Baudot CHU Purpan
> 31052 Toulouse Cedex 03, France *
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] connectome for monkeys // fiber trajectories

[David Van Essen]

1) Connectome Workbench is routinely used to analyze NHP neuroimaging data 
(macaque, chimpanzee, marmoset) in a number of labs, and a growing number of 
datasets are available in BALSA. See, for example:
Autio et al. (2019) https://www.biorxiv.org/content/10.1101/602979v1 

Donahue et al (2016) https://balsa.wustl.edu/study/show/W336 which includes 
probabilistic tractography.
Donahue et al  (PNAS 2018) https://balsa.wustl.edu/study/show/zlVX
Burt et al (Nat Neurosci 2018) https://balsa.wustl.edu/study/show/Kx5n

2) Caret is now a legacy platform.  File conversion options are available for 
converting to wb_view format.

3) Last year’s HCP course included a practical using NHP data 
(https://store.humanconnectome.org/courses/2018/exploring-the-human-connectome.php)
 
There will be some coverage of NHP analyses in this year’s course 
(https://store.humanconnectome.org/courses/2019/exploring-the-human-connectome.php)

David

> On Apr 11, 2019, at 9:19 AM, DE CASTRO Vanessa  
> wrote:
> 
> Hi! I've started to work with the human connectome workbench, and I was 
> wondering if is ready to use with monkeys as well, like Caret. 
> 
> And I also read in the tutorial that you are already working in a new 
> feature: probabilistic fiber trajectories... how soon it will come?? :D
> 
> Thank you very much for everything.
> 
> Sinceresly yours,
> 
> --
> 
> Vanessa DeCastro, PhD
> Centre de Recherche Cerveau et Cognition - UMR 5549 - CNRS
> Pavillon Baudot CHU Purpan
> 31052 Toulouse Cedex 03, France 
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org 
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> 

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