The diffusion data are in the subjects native (T1w) space.  You just need to 
use surfaces that are also in that space (e.g. the surfaces in 
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k).  I would recommend using the 
white surface for counting and the pial surface for stopping.

As for the exact command, I would use the link I posted to figure that out as I 
haven’t tried to do this yet.  Also, perhaps one of our diffusion colleagues 
might post some help too.

Peace,

Matt.

From: Max Bertolero <mb3...@seas.upenn.edu<mailto:mb3...@seas.upenn.edu>>
Date: Tuesday, August 1, 2017 at 2:10 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] fslr32k or fsaverage parcellation as seeds for 
probtrackx2

Thanks!

Right, the parcellation stuff seems pretty easy, but how to call the 
probtrackx2 with those label files is a bit trickier.

Do you have an example FSL command for a HCP subject? I can’t really figure out 
what I need to do, and what HCP has already done. For example, do any 
transforms need to be calculated? Do I just need the subject surface to 
fsaverage transform?

Thanks again,
Max

On Aug 1, 2017, at 2:51 PM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:

You can use wb_command -cifti-separate to get GIFTI label files out and then 
use https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Using_surfaces

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Max Bertolero 
<mb3...@seas.upenn.edu<mailto:mb3...@seas.upenn.edu>>
Date: Tuesday, August 1, 2017 at 1:40 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] fslr32k or fsaverage parcellation as seeds for probtrackx2

If I want to use a fslr32k (or fsaverage) parcellation as seeds for 
probtrackx2, does anyone know how do this on the command line?

For example, I would want to use this fsLR32k parcellation: 
https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/HCP/fslr32k/cifti/Schaefer2018_400Parcels_17Networks_order.dlabel.nii

Thanks!
Max Bertolero, PhD
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