Re: [HCP-Users] wb_command -metric-rois-from-extrema

2018-06-08 Thread Timothy Coalson 
If -metric-stats produces more than one number, then the input file had
more than one map.

Tim


On Fri, Jun 8, 2018 at 4:16 AM, Xinyang Liu  wrote:

> Dear Tim, dear Glasser,
>
> Thank you very much for your answers. That's very clear to me now. :)
>
> By the way, I also have a question when counting the vertex number of
> surface ROIs (.func.gii) using the wb_command -metric-stats -reduce SUM. Among
> around 200 subjects, there are two subjects whose vertex number outcomes
> are two sum values (e.g. 63 97 in a column), which is strange. Do you know
> the possible reason for that? Thanks.
>
> Best regards,
> Xinyang
>
>
> At 2018-06-08 05:15:36, "Timothy Coalson"  wrote:
>
> A picture is worth a thousand words, so here is a single subject 32k fs_LR
> surface, rendered to show edges between vertices, showing the variable
> spacing (you can check this on other surfaces by loading them in wb_view,
> and going to the Surface menu, clicking Properties, and setting "Drawin
> Type" to "Links (Edges)".
>
> In short, you shouldn't think of vertices like you do voxels, they don't
> use a fully regular grid.  This is why wb_command spatial operations take
> nearly all distances in mm, not in neighbors.
>
> Tim
>
>
> On Thu, Jun 7, 2018 at 10:48 AM, Glasser, Matthew 
> wrote:
>
>> On a standard mesh anatomical surface the vertex spacing is non-uniform
>> across the surface.  If you used the spheres you could get a uniform number
>> of vertices (though now the patches would cover different total areas).
>> Probably the uniform in mm approach (on the midthickness with appropriate
>> correction for shrinkage by vertex areas) is what you want.
>>
>> Peace,
>>
>> Matt.
>>
>> From:  on behalf of Xinyang Liu <
>> xinyang_ie...@163.com>
>> Date: Thursday, June 7, 2018 at 8:33 AM
>> To: HCP 讨论组 
>> Subject: [HCP-Users] wb_command -metric-rois-from-extrema
>>
>> Dear HCP experts,
>>
>> Hi. I have some confusions when using the workbench command
>> *-metric-rois-from-extrema*. When using it to draw ROIs on the fMRI
>> surface, I found that with the same radium, the number of vertices inside
>> the ROI can be different in different locations. For example, when r=5mm,
>> the vertex number can range from around 30 to around 80. Maybe I do not
>> understand very well about the parameter  - geodesic distance
>> limit from vertex, in mm. My understanding is that the distance is the
>> radium around the extrema on the stretched surface, and the vertex numbers
>> should be the same after the radium is set. Where do I misunderstand?
>>
>> Look forward to any kind guidance. Thanks a lot.
>>
>> Best regards,
>> Xinyang
>>
>>
>>
>>
>>
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>
>
>
>
>

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Re: [HCP-Users] wb_command -metric-rois-from-extrema

2018-06-08 Thread Xinyang Liu 
Dear Tim, dear Glasser,


Thank you very much for your answers. That's very clear to me now. :)


By the way, I also have a question when counting the vertex number of surface 
ROIs (.func.gii) using the wb_command -metric-stats -reduce SUM. Among around 
200 subjects, there are two subjects whose vertex number outcomes are two sum 
values (e.g. 63 97 in a column), which is strange. Do you know the possible 
reason for that? Thanks.


Best regards,
Xinyang



At 2018-06-08 05:15:36, "Timothy Coalson"  wrote:

A picture is worth a thousand words, so here is a single subject 32k fs_LR 
surface, rendered to show edges between vertices, showing the variable spacing 
(you can check this on other surfaces by loading them in wb_view, and going to 
the Surface menu, clicking Properties, and setting "Drawin Type" to "Links 
(Edges)".


In short, you shouldn't think of vertices like you do voxels, they don't use a 
fully regular grid.  This is why wb_command spatial operations take nearly all 
distances in mm, not in neighbors.



Tim




On Thu, Jun 7, 2018 at 10:48 AM, Glasser, Matthew  wrote:

On a standard mesh anatomical surface the vertex spacing is non-uniform across 
the surface.  If you used the spheres you could get a uniform number of 
vertices (though now the patches would cover different total areas).  Probably 
the uniform in mm approach (on the midthickness with appropriate correction for 
shrinkage by vertex areas) is what you want.


Peace,


Matt.


From:  on behalf of Xinyang Liu 

Date: Thursday, June 7, 2018 at 8:33 AM
To: HCP 讨论组 
Subject: [HCP-Users] wb_command -metric-rois-from-extrema



Dear HCP experts,


Hi. I have some confusions when using the workbench command 
-metric-rois-from-extrema. When using it to draw ROIs on the fMRI surface, I 
found that with the same radium, the number of vertices inside the ROI can be 
different in different locations. For example, when r=5mm, the vertex number 
can range from around 30 to around 80. Maybe I do not understand very well 
about the parameter  - geodesic distance limit from vertex, in mm. My 
understanding is that the distance is the radium around the extrema on the 
stretched surface, and the vertex numbers should be the same after the radium 
is set. Where do I misunderstand?


Look forward to any kind guidance. Thanks a lot.


Best regards,
Xinyang






 

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Re: [HCP-Users] wb_command -metric-rois-from-extrema

2018-06-07 Thread Glasser, Matthew 
On a standard mesh anatomical surface the vertex spacing is non-uniform across 
the surface.  If you used the spheres you could get a uniform number of 
vertices (though now the patches would cover different total areas).  Probably 
the uniform in mm approach (on the midthickness with appropriate correction for 
shrinkage by vertex areas) is what you want.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Thursday, June 7, 2018 at 8:33 AM
To: HCP 讨论组 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] wb_command -metric-rois-from-extrema

Dear HCP experts,

Hi. I have some confusions when using the workbench command 
-metric-rois-from-extrema. When using it to draw ROIs on the fMRI surface, I 
found that with the same radium, the number of vertices inside the ROI can be 
different in different locations. For example, when r=5mm, the vertex number 
can range from around 30 to around 80. Maybe I do not understand very well 
about the parameter  - geodesic distance limit from vertex, in mm. My 
understanding is that the distance is the radium around the extrema on the 
stretched surface, and the vertex numbers should be the same after the radium 
is set. Where do I misunderstand?

Look forward to any kind guidance. Thanks a lot.

Best regards,
Xinyang






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