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 <file>".  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 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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