Re: [HCP-Users] using surfaces as termination masks

[Timothy Coalson]

You can count the number of vertices in an ROI metric file with wb_command
-metric-stats using SUM (the ROI should be the input, you don't need -roi).

Tim


On Tue, Apr 17, 2018 at 7:31 AM, Xinyang Liu <xinyang_ie...@163.com> wrote:

> Dear Matt, dear Tim,
>
> Lots of thanks! I have a better understanding now owing to your detailed
> explanation. :)
> By the way, is there any command in the workbench to count the vertex
> number on single surface ROI?
>
> Best regards,
> Xinyang
>
>
> At 2018-04-17 08:11:23, "Glasser, Matthew" <glass...@wustl.edu> wrote:
>
> It is better to have the termination surface outside the counting surface
> (e.g. count on white, terminate on pial).  I do not remember if they can be
> the same surface or not, so you would need to ask this on the FSL list.
>
> Peace,
>
> Matt.
>
> From: Timothy Coalson <tsc...@mst.edu>
> Date: Monday, April 16, 2018 at 4:10 PM
> To: Xinyang Liu <xinyang_ie...@163.com>
> Cc: HCP 讨论组 <hcp-users@humanconnectome.org>, Matt Glasser <
> glass...@wustl.edu>
> Subject: Re: [HCP-Users] using surfaces as termination masks
>
> Inline replies.
>
> Tim
>
> On Sun, Apr 15, 2018 at 9:42 AM, Xinyang Liu <xinyang_ie...@163.com>
> wrote:
>
>> Dear Matt, dear Tim,
>>
>> Very grateful for both of your kind replies. :)
>>
>> Here are some further questions based on your feedbacks.
>>
>> 1. For the ROI of neocortex (atlasroi.shape.gii), does it mean this
>> shape file includes pial, midthickness and white surfaces? I previously
>> thought the .shape.gii file provides cortical shape information, like
>> curvature.  But then I found the value of each atlasroi vertex is 1. Is
>> it just an atlas map? Why was it chosen to set the value of L/R white.asc
>> in surf2surf for brain surfaces? How do we usually give the --values in
>> surf2surf?
>>
>
> .shape.gii is a file extension, it does not tell you what is in the file.
> It is actually the same file format as .func.gii, and we are not entirely
> consistent about when we choose to use each one.  "atlasroi.shape.gii" is
> just a binary roi, as "atlasroi" is intended to imply - it has values of 1
> on vertices that get used in our standard cifti space, and 0 on vertices
> that don't get used.  There are no coordinates or topology in it, no white,
> no pial, no midthickness - it is not a .surf.gii file, and we don't use the
> "combined data and coordinates" type files that other software does
> (unfortunately, probtrackx requires such "combined" files, adding to your
> confusion).  In workbench, surfaces are always loaded from a different file
> than the data to display on them.
>
>
>> 2. For the CIFTI and GIFTI matrices, I didn't intend to get the value of
>> each element, but preferred to know what kind of data is stored, which
>> might be shown by the name of each column, or data can be recognized as
>> coordinates. I am wondering how to check this.
>>
>
> They can store any type of measure.  You can get the names of the maps, if
> they have been named at all, by using "wb_command -file-information
> -only-map-names ".  Cifti files only store data values, and do not
> additionally contain surface coordinates or topology.  You have to load
> surfaces separately from the cifti file.
>
>
>> 3. I could not understand well that the cortex ROI would allow
>> connections to pass through the medial wall. Because when looking at the
>> surface outlines of "L/R.white.32k_fs_LR.surf.gii", it seems that the
>> left and white surfaces are closed regions (please see the figure
>> attached). Then how do connections pass through the middle surfaces?
>>
>
> The atlasroi.shape.gii has values of 0 on the vertices that cut through
> the corpus callosum - if you generate the files correctly, the tractography
> software will see these values of 0 and know not to terminate a streamline
> that hits the surface where the value is 0, and continue until it hits a
> vertex with a value of 1.  You will need to specify the files for both
> hemispheres to the tractography command, I assume.
>
>
>> 4. If we acquire seed ROIs from the midthickness surface, does it mean
>> that the termination surface masks can only come from the pial surface
>> then? Because the white surface is in the inner layer and therefore would
>> stop the streamlines coming from the mid-surface to go inside the brain. Is
>> my understanding correct?
>>
>
> I don't understand this question.  I don't know if it is even possible to
> specify multiple stopping surfaces for one hemispher

Re: [HCP-Users] using surfaces as termination masks

[Xinyang Liu]

Dear Matt, dear Tim,


Lots of thanks! I have a better understanding now owing to your detailed 
explanation. :)
By the way, is there any command in the workbench to count the vertex number on 
single surface ROI?


Best regards,
Xinyang




At 2018-04-17 08:11:23, "Glasser, Matthew" <glass...@wustl.edu> wrote:

It is better to have the termination surface outside the counting surface (e.g. 
count on white, terminate on pial).  I do not remember if they can be the same 
surface or not, so you would need to ask this on the FSL list.


Peace,


Matt.


From: Timothy Coalson <tsc...@mst.edu>
Date: Monday, April 16, 2018 at 4:10 PM
To: Xinyang Liu <xinyang_ie...@163.com>
Cc: HCP 讨论组 <hcp-users@humanconnectome.org>, Matt Glasser <glass...@wustl.edu>
Subject: Re: [HCP-Users] using surfaces as termination masks



Inline replies.


Tim



On Sun, Apr 15, 2018 at 9:42 AM, Xinyang Liu <xinyang_ie...@163.com> wrote:

Dear Matt, dear Tim,


Very grateful for both of your kind replies. :)


Here are some further questions based on your feedbacks.


1. For the ROI of neocortex (atlasroi.shape.gii), does it mean this shape file 
includes pial, midthickness and white surfaces? I previously thought the 
.shape.gii file provides cortical shape information, like curvature.  But then 
I found the value of each atlasroi vertex is 1. Is it just an atlas map? Why 
was it chosen to set the value of L/R white.asc in surf2surf for brain 
surfaces? How do we usually give the --values in surf2surf?


.shape.gii is a file extension, it does not tell you what is in the file.  It 
is actually the same file format as .func.gii, and we are not entirely 
consistent about when we choose to use each one.  "atlasroi.shape.gii" is just 
a binary roi, as "atlasroi" is intended to imply - it has values of 1 on 
vertices that get used in our standard cifti space, and 0 on vertices that 
don't get used.  There are no coordinates or topology in it, no white, no pial, 
no midthickness - it is not a .surf.gii file, and we don't use the "combined 
data and coordinates" type files that other software does (unfortunately, 
probtrackx requires such "combined" files, adding to your confusion).  In 
workbench, surfaces are always loaded from a different file than the data to 
display on them.
 
2. For the CIFTI and GIFTI matrices, I didn't intend to get the value of each 
element, but preferred to know what kind of data is stored, which might be 
shown by the name of each column, or data can be recognized as coordinates. I 
am wondering how to check this.


They can store any type of measure.  You can get the names of the maps, if they 
have been named at all, by using "wb_command -file-information -only-map-names 
".  Cifti files only store data values, and do not additionally contain 
surface coordinates or topology.  You have to load surfaces separately from the 
cifti file.
 
3. I could not understand well that the cortex ROI would allow connections to 
pass through the medial wall. Because when looking at the surface outlines of 
"L/R.white.32k_fs_LR.surf.gii", it seems that the left and white surfaces are 
closed regions (please see the figure attached). Then how do connections pass 
through the middle surfaces?


The atlasroi.shape.gii has values of 0 on the vertices that cut through the 
corpus callosum - if you generate the files correctly, the tractography 
software will see these values of 0 and know not to terminate a streamline that 
hits the surface where the value is 0, and continue until it hits a vertex with 
a value of 1.  You will need to specify the files for both hemispheres to the 
tractography command, I assume.
 
4. If we acquire seed ROIs from the midthickness surface, does it mean that the 
termination surface masks can only come from the pial surface then? Because the 
white surface is in the inner layer and therefore would stop the streamlines 
coming from the mid-surface to go inside the brain. Is my understanding correct?


I don't understand this question.  I don't know if it is even possible to 
specify multiple stopping surfaces for one hemisphere in probtrackx.  If it 
were, and you used the white surface as one of them, then it should stop all 
streamlines before they reach midthickness or pial (unless you did something 
wrong).  I think the general guidance is to use the white matter surface, as 
fiber directions become less reliable in gray matter.
 
Look forward to your further guidance. Many thanks!


Best regards,
Xinyang





At 2018-04-14 05:42:36, "Timothy Coalson" <tsc...@mst.edu> wrote:

Inline comment.


Tim


On Thu, Apr 12, 2018 at 11:01 PM, Xinyang Liu <xinyang_ie...@163.com> wrote:



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.


Gifti files, and dense cifti files, have too many e

Re: [HCP-Users] using surfaces as termination masks

[Glasser, Matthew]

It is better to have the termination surface outside the counting surface (e.g. 
count on white, terminate on pial).  I do not remember if they can be the same 
surface or not, so you would need to ask this on the FSL list.

Peace,

Matt.

From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Monday, April 16, 2018 at 4:10 PM
To: Xinyang Liu <xinyang_ie...@163.com<mailto:xinyang_ie...@163.com>>
Cc: HCP 讨论组 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, Matt 
Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] using surfaces as termination masks

Inline replies.

Tim

On Sun, Apr 15, 2018 at 9:42 AM, Xinyang Liu 
<xinyang_ie...@163.com<mailto:xinyang_ie...@163.com>> wrote:
Dear Matt, dear Tim,

Very grateful for both of your kind replies. :)

Here are some further questions based on your feedbacks.

1. For the ROI of neocortex (atlasroi.shape.gii), does it mean this shape file 
includes pial, midthickness and white surfaces? I previously thought the 
.shape.gii file provides cortical shape information, like curvature.  But then 
I found the value of each atlasroi vertex is 1. Is it just an atlas map? Why 
was it chosen to set the value of L/R white.asc in surf2surf for brain 
surfaces? How do we usually give the --values in surf2surf?

.shape.gii is a file extension, it does not tell you what is in the file.  It 
is actually the same file format as .func.gii, and we are not entirely 
consistent about when we choose to use each one.  "atlasroi.shape.gii" is just 
a binary roi, as "atlasroi" is intended to imply - it has values of 1 on 
vertices that get used in our standard cifti space, and 0 on vertices that 
don't get used.  There are no coordinates or topology in it, no white, no pial, 
no midthickness - it is not a .surf.gii file, and we don't use the "combined 
data and coordinates" type files that other software does (unfortunately, 
probtrackx requires such "combined" files, adding to your confusion).  In 
workbench, surfaces are always loaded from a different file than the data to 
display on them.

2. For the CIFTI and GIFTI matrices, I didn't intend to get the value of each 
element, but preferred to know what kind of data is stored, which might be 
shown by the name of each column, or data can be recognized as coordinates. I 
am wondering how to check this.

They can store any type of measure.  You can get the names of the maps, if they 
have been named at all, by using "wb_command -file-information -only-map-names 
".  Cifti files only store data values, and do not additionally contain 
surface coordinates or topology.  You have to load surfaces separately from the 
cifti file.

3. I could not understand well that the cortex ROI would allow connections to 
pass through the medial wall. Because when looking at the surface outlines of 
"L/R.white.32k_fs_LR.surf.gii", it seems that the left and white surfaces are 
closed regions (please see the figure attached). Then how do connections pass 
through the middle surfaces?

The atlasroi.shape.gii has values of 0 on the vertices that cut through the 
corpus callosum - if you generate the files correctly, the tractography 
software will see these values of 0 and know not to terminate a streamline that 
hits the surface where the value is 0, and continue until it hits a vertex with 
a value of 1.  You will need to specify the files for both hemispheres to the 
tractography command, I assume.

4. If we acquire seed ROIs from the midthickness surface, does it mean that the 
termination surface masks can only come from the pial surface then? Because the 
white surface is in the inner layer and therefore would stop the streamlines 
coming from the mid-surface to go inside the brain. Is my understanding correct?

I don't understand this question.  I don't know if it is even possible to 
specify multiple stopping surfaces for one hemisphere in probtrackx.  If it 
were, and you used the white surface as one of them, then it should stop all 
streamlines before they reach midthickness or pial (unless you did something 
wrong).  I think the general guidance is to use the white matter surface, as 
fiber directions become less reliable in gray matter.

Look forward to your further guidance. Many thanks!

Best regards,
Xinyang



At 2018-04-14 05:42:36, "Timothy Coalson" 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:
Inline comment.

Tim

On Thu, Apr 12, 2018 at 11:01 PM, Xinyang Liu 
<xinyang_ie...@163.com<mailto:xinyang_ie...@163.com>> wrote:

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.

Gifti files, and dense cifti files, have too many elements to be properly 
viewed as a matrix, and the vertices that are adjacent in the file data don't 
make much s

Re: [HCP-Users] using surfaces as termination masks

[Timothy Coalson]

Inline replies.

Tim

On Sun, Apr 15, 2018 at 9:42 AM, Xinyang Liu  wrote:

> Dear Matt, dear Tim,
>
> Very grateful for both of your kind replies. :)
>
> Here are some further questions based on your feedbacks.
>
> 1. For the ROI of neocortex (atlasroi.shape.gii), does it mean this shape
> file includes pial, midthickness and white surfaces? I previously thought
> the .shape.gii file provides cortical shape information, like curvature.
> But then I found the value of each atlasroi vertex is 1. Is it just an
> atlas map? Why was it chosen to set the value of L/R white.asc in surf2surf
> for brain surfaces? How do we usually give the --values in surf2surf?
>

.shape.gii is a file extension, it does not tell you what is in the file.
It is actually the same file format as .func.gii, and we are not entirely
consistent about when we choose to use each one.  "atlasroi.shape.gii" is
just a binary roi, as "atlasroi" is intended to imply - it has values of 1
on vertices that get used in our standard cifti space, and 0 on vertices
that don't get used.  There are no coordinates or topology in it, no white,
no pial, no midthickness - it is not a .surf.gii file, and we don't use the
"combined data and coordinates" type files that other software does
(unfortunately, probtrackx requires such "combined" files, adding to your
confusion).  In workbench, surfaces are always loaded from a different file
than the data to display on them.


> 2. For the CIFTI and GIFTI matrices, I didn't intend to get the value of
> each element, but preferred to know what kind of data is stored, which
> might be shown by the name of each column, or data can be recognized as
> coordinates. I am wondering how to check this.
>

They can store any type of measure.  You can get the names of the maps, if
they have been named at all, by using "wb_command -file-information
-only-map-names ".  Cifti files only store data values, and do not
additionally contain surface coordinates or topology.  You have to load
surfaces separately from the cifti file.


> 3. I could not understand well that the cortex ROI would allow
> connections to pass through the medial wall. Because when looking at the
> surface outlines of "L/R.white.32k_fs_LR.surf.gii", it seems that the
> left and white surfaces are closed regions (please see the figure
> attached). Then how do connections pass through the middle surfaces?
>

The atlasroi.shape.gii has values of 0 on the vertices that cut through the
corpus callosum - if you generate the files correctly, the tractography
software will see these values of 0 and know not to terminate a streamline
that hits the surface where the value is 0, and continue until it hits a
vertex with a value of 1.  You will need to specify the files for both
hemispheres to the tractography command, I assume.


> 4. If we acquire seed ROIs from the midthickness surface, does it mean
> that the termination surface masks can only come from the pial surface
> then? Because the white surface is in the inner layer and therefore would
> stop the streamlines coming from the mid-surface to go inside the brain. Is
> my understanding correct?
>

I don't understand this question.  I don't know if it is even possible to
specify multiple stopping surfaces for one hemisphere in probtrackx.  If it
were, and you used the white surface as one of them, then it should stop
all streamlines before they reach midthickness or pial (unless you did
something wrong).  I think the general guidance is to use the white matter
surface, as fiber directions become less reliable in gray matter.


> Look forward to your further guidance. Many thanks!
>
> Best regards,
> Xinyang
>
>
>
> At 2018-04-14 05:42:36, "Timothy Coalson"  wrote:
>
> Inline comment.
>
> Tim
>
> On Thu, Apr 12, 2018 at 11:01 PM, Xinyang Liu 
> wrote:
>
>>
>> 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.
>>
>
> Gifti files, and dense cifti files, have too many elements to be properly
> viewed as a matrix, and the vertices that are adjacent in the file data
> don't make much sense spatially.  If you want a matrix display, you should
> use a parcellated cifti file (which can be made from a dense cifti file
> with wb_command -cifti-parcellate).
>
> Tim
>
>
> 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.
>
>
>
>
>
>
>
>
>

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Re: [HCP-Users] using surfaces as termination masks

[Timothy Coalson]

Inline comment.

Tim

On Thu, Apr 12, 2018 at 11:01 PM, Xinyang Liu  wrote:

>
> 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.
>

Gifti files, and dense cifti files, have too many elements to be properly
viewed as a matrix, and the vertices that are adjacent in the file data
don't make much sense spatially.  If you want a matrix display, you should
use a parcellated cifti file (which can be made from a dense cifti file
with wb_command -cifti-parcellate).

Tim

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Re: [HCP-Users] using surfaces as termination masks

[Glasser, Matthew]

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: 
>
 on behalf of Xinyang Liu >
Date: Thursday, April 12, 2018 at 11:01 PM
To: HCP 讨论组 
>
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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