1.  That is the ROI of neocortex (excluding the medial wall).  The medial wall 
is the non-cortical tissue that connects the two hemispheres (e.g. corpus 
callosum, diencephalon).  All of the surface meshes are usable if they are the 
same kind of mesh (i.e. native, 32k, 164k).

2.  You can convert them to dconn files with wb_command -probtrackx-dot-convert.

3.  The cortex ROI will allow connections to pass through the medial wall.  You 
can include multiple surface and volume ROIs in probtrackx.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Xinyang Liu <xinyang_ie...@163.com<mailto:xinyang_ie...@163.com>>
Date: Thursday, April 12, 2018 at 11:01 PM
To: HCP 讨论组 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] using surfaces as termination masks

Dear HCP experts,

Hi. I have some questions when using cortical surfaces as termination masks in 
global fibre tracking. They are listed as follows.

1. In one HCP course tutorial, the example uses WM/GM boundary as termination 
masks to prevent implausible jumps. The command is
"surf2surf -i fsaverage_LR32k/100307.L.white.32k_fs_LR.surf.gii  -o L.white.asc 
--outputtype=ASCII 
--values=fsaverage_LR32k/100307.L.atlasroi.32k_fs_LR.shape.gii "

I am not very clear what this atlasroi.shape.gii file means. I checked previous 
HCP emails and found that it corresponds to the "medial wall". So the question 
is, which layer of surface does this medial wall correspond to? And if I want 
to use pial or midthickness surface also as masks, should I also use the same 
"atlasroi" file as --values?

2. How to look at the CIFTI and GIFTI files as matrices? I haven't found a 
proper way to look at the information inside as rows and columns.

3. The cortical surface layers are always separated into left(.L) and right(.R) 
 hemispheres  in HCP data files. But is there any type of brain surface that I 
can use as a whole termination mask in global fibre tracking? Since the left 
and right hemispheres also exist connections between each other, the fibre 
would be stopped half-way if using half-hemisphere surface to terminate.

Look forward to any kind guidance. Thank you very much.

Best regards,
Xinyang






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