On Mon, Aug 11, 2014 at 2:14 PM, Tang, Yan <[email protected]> wrote:
> Yes，I have a lot of volumes which need be projected to surface. I only
> know how to use the 'map volume to surface '. I don't know how to use the
> command. Could you give me an example?
> Can the file of *.coord.gii be thought as the <coordinate-file-name> file?
> But I only found .coord file can be used in the menu of "caret command
> executor" . How about "topo"?
>
.coord.gii should work, if it doesn't rename or copy the file to end in
just .coord . The topo is the same file you need to load to be able to
view the surface.
> another thing is how to set the <input-metric-or-paint-file-name>?
>
>From the pasted help:
"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."
In other words, if you don't want to append the columns to an existing
metric file, use "" (a pair of double quotes) for the argument.
Since you asked something related on the hcp_users list (wb_command volume
to surface mapping), I will recommend that you try using wb_command for
this, as caret5 is no longer under active development. The main hurdle in
moving to Workbench is converting the separate coord/topo files into the
combined .surf.gii format (with caret_command -file-convert with the -sc
option).
> ________________________________________
> From: [email protected] [
> [email protected]] on behalf of Donna Dierker [
> [email protected]]
> Sent: Tuesday, August 05, 2014 9:14 AM
> To: Caret, SureFit, and SuMS software users
> Cc: Tang, Yiyuan
> Subject: 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
> <coordinate-file-name>
> <topology-file-name>
> <input-metric-or-paint-file-name>
> <output-metric-or-paint-file-name>
> <algorithm>
> <input-volume-file-names>
> [-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" <[email protected]> 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: [email protected] [
> [email protected]] on behalf of Donna Dierker [
> [email protected]]
> > 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" <[email protected]> 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: [email protected] [
> [email protected]] on behalf of Donna Dierker [
> [email protected]]
> >> 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" <[email protected]> wrote:
> >>
> >>> I am sure that the file exist and the size of file is 446KB. Is It
> correct?
> >>> ________________________________________
> >>> From: [email protected] [
> [email protected]] on behalf of Donna Dierker [
> [email protected]]
> >>> 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" <[email protected]> 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
> >>>> [email protected]
> >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >>>
> >>>
> >>> _______________________________________________
> >>> caret-users mailing list
> >>> [email protected]
> >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >>>
> >>> _______________________________________________
> >>> caret-users mailing list
> >>> [email protected]
> >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >>
> >>
> >> _______________________________________________
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> >> [email protected]
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> >
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> >
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