[caret-users] projecting functional MRI to gii surfaces

Donna Dierker donna at brainvis.wustl.edu
Wed Aug 13 14:27:41 CDT 2014


Hi Yan,

I'm not sure about wb_import, but I know it won't downsample for you.  This will, I hope:

http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/FSLR/downsample164_to_32k.zip
login pub
password download

There is a script in there you will need to tweak to put in your pathnames and subject list.  I tried it on some freesurfer_to_fs_LR output I had lying around, and it worked.  The zip file also contains the spheres you need:

ExtractDir=/home/donna/downsample164_to_32k
SubjectDir=/mnt/myelin/donna/SUBJ/fs_LR_output_directory
ResamplingMethod=BARYCENTRIC

for Subject in $SubjList
do
 for Hemisphere in L R
 do
   CoordInput=$SubjectDir/$Subject/"$Subject".$Hemisphere.midthickness_orig.164k_fs_LR.coord.gii
   TopoInput=$SubjectDir/$Subject/"$Subject".$Hemisphere.164k_fs_LR.topo.gii
   SurfaceInput=$SubjectDir/$Subject/"$Subject".$Hemisphere.midthickness_orig.164k_fs_LR.surf.gii
   caret_command -file-convert -sc -is CARET $CoordInput $TopoInput -os
GS $SurfaceInput
   CurrentSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.164k_fs_LR.surf.gii
   NewSphere=$ExtractDir/spheres/standard.$Hemisphere.sphere.32k_fs_LR.surf.gii
   SurfaceOutput=$SubjectDir/$Subject/"$Subject".$Hemisphere.midthickness_orig.32k_fs_LR.surf.gii
   wb_command -surface-resample \
	$SurfaceInput \
	$CurrentSphere \
	$NewSphere \
	$ResamplingMethod \
	$SurfaceOutput
 done
done

Donna


On Aug 13, 2014, at 10:42 AM, "Tang, Yan" <yan.tang at ttu.edu> wrote:

> You means I can finish this work by using the Connectome Workbench. So, the first thing I need to do is to convert all files to Workbench format by using wb_import. Is it true?
> From: caret-users-bounces at brainvis.wustl.edu [caret-users-bounces at brainvis.wustl.edu] on behalf of Timothy Coalson [tsc5yc at mst.edu]
> Sent: Tuesday, August 12, 2014 7:16 PM
> To: Caret, SureFit, and SuMS software users; Donna Dierker
> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
> 
> -spec-file-change-resolution will not get you to the fs_LR 32k atlas from fs_LR 164k (but it may get you deceptively close, making it even more treacherous).  Those messages aren't errors, and the reasons behind them are better left alone, as this isn't the command you want.
> 
> What you need to do is to use the fs_LR atlas files for resampling the surface.  In caret5, this requires deformation map files, which we have probably already made for going between fs_LR 32k and 164k (Donna, do you know if these are available?), with the -deformation-map-apply command.  However, we now do this in Connectome Workbench using atlas spheres directly with the -surface-resample command (the fs_LR 32k and 164k spheres are aligned by definition, but going to or from other atlases will need a cross-atlas registered sphere).
> 
> Tim
> 
> 
> 
> On Tue, Aug 12, 2014 at 4:33 PM, Tang, Yan <yan.tang at ttu.edu> wrote:
> Sorry, I meet another problem.  I used  the Freesurfer_to_fs_LR Pipeline to get  164k fs_LR surface. I think the vertex too much. So I want to  down-sampled to a 32,492 vertex surface. I used the caret_command -spec-file-change-resolution. 
> But, the error was  followed:
> "Nonstandard resolution specified...
> Using closest divided icosahedron, with 32492 nodes."
> Can you explain it?
> if I change the number, I find only  a few files be created such as def_sphere.coord, def_sphere.deform_map,study1.R.2k_fs_LR.topo.gii and study1.R.mini+orig.2k_fs_LR.spc. Many files such as curvature.shape.gii, inflated.coord.gii, midthickness.coord.gii, pial.coord.gii, thickness.shape.gii and white.coord.gii all aren't changed. So, I do some wrong steps. How should I do it?
> From: caret-users-bounces at brainvis.wustl.edu [caret-users-bounces at brainvis.wustl.edu] on behalf of Timothy Coalson [tsc5yc at mst.edu]
> Sent: Monday, August 11, 2014 3:54 PM
> 
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
> 
> 
> On Mon, Aug 11, 2014 at 2:14 PM, Tang, Yan <yan.tang at ttu.edu> 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: caret-users-bounces at brainvis.wustl.edu [caret-users-bounces at brainvis.wustl.edu] on behalf of Donna Dierker [donna at brainvis.wustl.edu]
> 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" <yan.tang at ttu.edu> 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-bounces at brainvis.wustl.edu [caret-users-bounces at brainvis.wustl.edu] on behalf of Donna Dierker [donna.dierker at 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.tang at 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-bounces at brainvis.wustl.edu [caret-users-bounces at brainvis.wustl.edu] on behalf of Donna Dierker [donna.dierker at 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.tang at ttu.edu> wrote:
> >>
> >>> I am sure that the file exist and the size of file is 446KB. Is It correct?
> >>> ________________________________________
> >>> From: caret-users-bounces at brainvis.wustl.edu [caret-users-bounces at brainvis.wustl.edu] on behalf of Donna Dierker [donna.dierker at 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.tang at 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 at brainvis.wustl.edu
> >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >>>
> >>>
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> >>>
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> >>
> >>
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