There is a way to make probtrackx produce a deterministic like output, you can ask on the FSL list how to do that.
Peace,
Matt.
From: <Luo>, Yishan <lys84...@hotmail.com>
Date: Wednesday, May 7, 2014 at 4:39 AM To: Matt Glasser <glass...@wusm.wustl.edu>, Timothy Coalson <tsc...@mst.edu> Cc: Donna Dierker <do...@brainvis.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: RE: [HCP-Users] activation region mask Thanks very much for your suggestion. I found that FSL's probtrackx is probabilistic fiber tracking. And it is really slow, even with parallel computing.
What I need is only deterministic fiber tracking.
But I found most of deterministic fiber tracking tools don't accept gifti file as seed region.
So I am sorry still confused with the question, how to transfer a label.gii file into a volumetric *.nii file for easy use.
Thanks a lot!
Lisa
From: glass...@wusm.wustl.edu To: tsc...@mst.edu; lys84...@hotmail.com CC: do...@brainvis.wustl.edu; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] activation region mask Date: Fri, 2 May 2014 05:06:35 +0000 I would recommend FSL’s probtrackx for tractography and you can visualize the results in Connectome Workbench. I’ve never heard of dsistudio, so I don’t know how to help you use it. We don’t provide DSI data, but rather 3-shell HARDI data.
Peace,
Matt.
From: Timothy Coalson <tsc...@mst.edu>
Date: Thursday, May 1, 2014 at 10:30 PM To: "Luo,Yishan" <lys84...@hotmail.com> Cc: Matt Glasser <glass...@wusm.wustl.edu>, Donna Dierker <do...@brainvis.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] activation region mask The command is not asking you for a label name, it is asking you which surface you want, and the current options with our data are left cortex and right cortex. You asked it to find the "OTHER" surface, which doesn't exist ("nonexistant structure").
Our data has left and right cortex surface data in it to begin with, thresholding and importing to label doesn't change that. The label name you used in -cifti-label-import is irrelevant to this command. Use CORTEX_LEFT and CORTEX_RIGHT.
Tim
On Thu, May 1, 2014 at 10:09 PM, Luo,Yishan
<lys84...@hotmail.com> wrote:
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There is a way to make probtrackx produce a deterministic like output, you can ask on the FSL list how to do that.
Peace,
Matt.
From: <Luo>, Yishan <lys84...@hotmail.com>
Date: Wednesday, May 7, 2014 at 4:39 AM To: Matt Glasser <glass...@wusm.wustl.edu>, Timothy Coalson <tsc...@mst.edu> Cc: Donna Dierker <do...@brainvis.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: RE: [HCP-Users] activation region mask The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ |
- Re: [HCP-Users] activation region mask Timothy Coalson
- Re: [HCP-Users] activation region mask Glasser, Matthew
- Re: [HCP-Users] activation region mask Luo,Yishan
- Re: [HCP-Users] activation region mask Glasser, Matthew
- Re: [HCP-Users] activation region mask Luo,Yishan
- Re: [HCP-Users] activation region mask Timothy Coalson
- Re: [HCP-Users] activation region mask Luo,Yishan
- Re: [HCP-Users] activation region mask Timothy Coalson
- Re: [HCP-Users] activation region mask Glasser, Matthew
- Re: [HCP-Users] activation region mask Luo,Yishan
- Re: [HCP-Users] activation region mask Glasser, Matthew