Re: [caret-users] projecting functional MRI to gii surfaces
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" 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" 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" 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 >
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" 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" 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" 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" wrote: >>> >>
Re: [caret-users] projecting functional MRI to gii surfaces
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" 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" 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" 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 >> >> >> ___ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> ___ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ care
[caret-users] Metric file must be provided for the metric mapping
Yesterday, I ran into two arcane issues worth passing on, one of which was covered in an earlier thread: 1. First I tried mapping a paint volume onto an atlas surface, but it turned out the volume was scalar values -- not discrete integers as I'd expected for a label/ROI volume. Caret generated paint files that were just headers -- no data, but didn't complain. 2. After realizing these were scalars, I mapped as functional, but the mapping algorithm stayed on the paint-related algorithm, as Tony explains here: http://www.mail-archive.com/caret-users%40brainvis.wustl.edu/msg02887.html When I tried to map, I got the "Metric file must be provided for the metric mapping" error. Switching to a metric algorithm resolved the error. No action required; this is in case someone runs into the same issue and searches caret-users for answers. ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] projecting functional MRI to gii surfaces
I'm not clear on what you mean by "I want get fMRI time course for surface
vertices of every subject."
If you just mean how do you scale up -- map that many volumes to all your
subjects -- then I recommend scripting it and using caret_command. (Note that
Workbench, the software that is superseding Caret 5.*, has more robust mapping
features than caret_command, but I am going to provide the caret_command usage,
since this is the caret-users list. There is also a hcp-users list that covers
workbench.)
Here is the usage for the command that maps volumes onto surfaces:
caret_command -volume-map-to-surface
[-av average-voxel-neighbor-cube-size (mm)]
[-bf brain-fish-max-distance
brain-fish-splat factor]
[-g gaussian-neighbor-cube-size (mm)
sigma-norm
sigma-tang
norm below cutoff (mm)
norm above cutoff (mm)
tang-cutoff (mm)]
[-mv maximum-voxel-neighbor-cube-size (mm)]
[-sv strongest-voxel-neighbor-cube-size (mm)]
Map volume(s) to a surface metric or paint file.
For successful mapping, both the surface and the volume
must be in the same stereotaxic space.
"algorithm" is one of:
METRIC_AVERAGE_NODES
METRIC_AVERAGE_VOXEL
METRIC_ENCLOSING_VOXEL
METRIC_GAUSSIAN
METRIC_INTERPOLATED_VOXEL
METRIC_MAXIMUM_VOXEL
METRIC_MCW_BRAIN_FISH
METRIC_STRONGEST_VOXEL
PAINT_ENCLOSING_VOXEL
If the input metric or paint file name is not an empty string
(""), the newly create metric or paint columns will be
appended to the file and then written with the output file
name.
On Aug 4, 2014, at 3:49 PM, "Tang, Yan" wrote:
> Thank you for your help. Now, I meet another problem. I project all
> functional MRI to 164k fs_LR surface. Every subject have 135 volumes. I want
> get fMRI time course for surface vertices of every subject. 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 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" 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" 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 o
