Maybe I do some wrong things. I used the Freesurfer_to_fs_LR Pipeline to get
164k fs_LR surface. Then, I want to get the points in 164k fs_LR surface and
use these points as seed to analysis the resting state functional connectivity.
So I do project functional MRI to surface. But after that, I don't know how to
do it in next step. I get metric file, but these files cannot be read in
Matlab. And I also don't get the coordinates of the points in 164k fs_LR
surface.
Just you mention the method of Alex Cohen. I am beginner of Caret. Could you
tell me the method in detail?
thank you
________________________________________
From: caret-users-boun...@brainvis.wustl.edu
[caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
[do...@brainvis.wustl.edu]
Sent: Tuesday, August 05, 2014 10:26 AM
To: Caret, SureFit, and SuMS software users
Cc: Tang, Yiyuan
Subject: Re: [caret-users] projecting functional MRI to gii surfaces
You can do that, but I am not used to seeing this done with the mean
midthickness surface. Alex Cohen did something like this when he was using
resting state functional connectivity to find gradients in a subject's cortical
networks. He used the PALS flat or spherical map to get a common grid onto a
standard mesh. Once there, he projected that grid onto the individual's
midthickness surface on the standard mesh. (Like the grid is getting folded
back up into the individual's anatomical pattern.) Then he unprojected the
points to use as seeds for his analysis.
Do you mind if I ask how the mean midthickness surface comes into play?
Caret's Layers: Borders has options for making grids on the flat map. People
make grids on the sphere in matlab.
There are caret_command tools for unprojecting borders.
caret_command -surface-border-unprojection
Border files differ from border projection files in that they are points not
tied to a particular mesh. The advantage is that you can open the same border
point on, say, a native and 164k mesh, and it will align with both, if it
aligns with one (and they are identical except for mesh). The advantage of
borderproj files is that they open on multiple configurations - flat,
midthickness, inflated, etc. - but the price is that you're tied to a mesh.
On Aug 5, 2014, at 10:06 AM, "Tang, Yan" <yan.t...@ttu.edu> wrote:
> Thank you for your help. Another problem is how to use the Caret software to
> generate regularly spaced Cartesian grids on the flattened PALS-B12 average
> surface of the left and right hemispheres. Can I use this 3-dimensional (3D)
> stereotactic coordinates from the PALS-B12 average fiducial (midthickness)
> surface for each grid location to obtain the voxel coordinates (3 × 3 × 3 mm
> resolution) containing that point in fMRI?
>
> ________________________________________
> From: caret-users-boun...@brainvis.wustl.edu
> [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
> [donna.dier...@sbcglobal.net]
> Sent: Friday, August 01, 2014 5:34 PM
> To: Caret, SureFit, and SuMS software users
> Cc: Tang, Yiyuan
> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
>
> Push Toolbar: D/C and make sure the primary overlay is Metric.
>
> Make sure the right column is selected.
>
> If that check out okay, then I would do:
>
> File: Open Data File: Volume Functional File
> Load the volume you just mapped
> Switch to volume view and select view All (as opposed to H (horizontal or
> axial).
> Select D/C and on the page selection drop-down menu, scroll all the way to
> the bottom
> something like volume surface outline
> Toggle on the fiducial surface used for the mapping, so that you can see how
> the surface aligns with the volume.
>
> Sometimes there are header issues, and the origin is not set correctly,
> resulting in faulty volume-surface alignment.
>
>
> On Aug 1, 2014, at 4:29 PM, "Tang, Yan" <yan.t...@ttu.edu> wrote:
>
>> When I open the spec file and mapped the Metric, only the surface was
>> displayed. The result is in the attachment. How should I do?
>> ________________________________________
>> From: caret-users-boun...@brainvis.wustl.edu
>> [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
>> [donna.dier...@sbcglobal.net]
>> Sent: Friday, August 01, 2014 4:02 PM
>> To: Caret, SureFit, and SuMS software users
>> Cc: Tang, Yiyuan
>> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
>>
>> Hmmm. Sounds like more than a header to me.
>>
>> When you open the spec file you selected when you mapped the data, and
>> select the output file that is 446kb, what happens?
>>
>> You must make sure you select Metric on the D/C: Overlay/Underlay Surface
>> menu (primary or secondary, typically). Else it won't display.
>>
>>
>> On Aug 1, 2014, at 2:47 PM, "Tang, Yan" <yan.t...@ttu.edu> wrote:
>>
>>> I am sure that the file exist and the size of file is 446KB. Is It correct?
>>> ________________________________________
>>> From: caret-users-boun...@brainvis.wustl.edu
>>> [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
>>> [donna.dier...@sbcglobal.net]
>>> Sent: Friday, August 01, 2014 10:10 AM
>>> To: Caret, SureFit, and SuMS software users
>>> Cc: Tang, Yiyuan
>>> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
>>>
>>> Hi Yan,
>>>
>>> Could you use a terminal window or file manager to check whether the file
>>> exists, and if so, what its size is.
>>>
>>> We have seen cases before where the file was just a header -- no data.
>>> Inexplicably, the presence of a non-english character set on the system
>>> used has caused this sort of trouble. If there is a system nearby that
>>> does not have a non-english character set installed, you might see if Caret
>>> works there. Or remove any non-english character sets on your system and
>>> see if it helps.
>>>
>>> Donna
>>>
>>>
>>> On Jul 31, 2014, at 3:52 PM, "Tang, Yan" <yan.t...@ttu.edu> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Now I
>>>> want to map functional volumes to surfaces.
>>>> In volume selection page, I choose my file 'ff001_010.nii'; In spec file
>>>> and surface selection page, I choose the file 'study1.L.orig.164k_fs_LR'.
>>>> I get a file 'map_data_0_31_Jul_2014_15_10_13.metric'. But I find I
>>>> couldn't open this file. Which step is wrong? How can you do it?
>>>> _______________________________________________
>>>> caret-users mailing list
>>>> caret-users@brainvis.wustl.edu
>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>
>>>
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>>>
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>>
>>
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