Thank you very much! ________________________________ From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@mst.edu] Sent: Wednesday, August 06, 2014 5:18 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces
Yes, the vertices array appears to be the vertex coordinates. You may need to do the -file-convert -format-convert XML_BASE64_GZIP (not ASCII) on the metric file (and maybe even rename it to end in .func.gii) to load it in matlab as a gifti file. The metric file does not contain voxel values, it contains a value at each surface vertex. The correspondence between voxels and surface vertices is purely spatial, and unless you used enclosing voxel mapping (which is not good for continuous data values like functional activation), each vertex contains an interpolated value derived from several voxels. Tim On Wed, Aug 6, 2014 at 4:40 PM, Tang, Yan <yan.t...@ttu.edu<mailto:yan.t...@ttu.edu>> wrote: Thank you for your help. I use the command "caret_command -file-conver -sc -is CARET" to get surf.gii file. And I use the GIFTI to open this surf.gii file and get two important variables "vertices" and "faces". vertices= -6.8856 -52.5189 23.7218 -22.1394 -41.5367 68.0599 -49.4149 -0.5296 47.7317 -3.4733 22.7785 64.3392 -25.9901 -104.4682 4.0191 -47.4914 -56.3775 48.6392 -26.3158 45.2893 14.0113 -0.9479 9.1027 1.0427 -23.8312 -56.4579 -7.5924 -51.4654 -34.0955 1.4522 ............ I think the "vertices" include the coordinates. Is it right? But I still can't open the metric file in GIFTI. This metric file was obtain by mapping functional volumes to surfaces in volume selection page. When I used the caret_command -file-convert -format-convert ASCII my_fmri.metric, I found some information in the metric 0 -3.944756 1 0.000000 2 0.000000 3 0.000000 4 -0.291482 5 0.995688 6 6.848554 7 3.783060 8 0.804804 9 -4.805716 10 -6.419259 11 -0.036545 12 -5.132483 13 -6.023278 14 -6.115900 15 -6.208522 16 -6.301144 17 -6.347455 18 -5.193967 19 -3.463736 20 -2.005528 ................ These information maybe display the every voxel's value. But I still can't use the use the vertices in surf.gii as seed to analysis the resting state functional connectivity. Because I don't know the correspondence between the vertices in surf.gii and the voxel in fMRI. Please help me. Thank you. ________________________________ From: caret-users-boun...@brainvis.wustl.edu<mailto:caret-users-boun...@brainvis.wustl.edu> [caret-users-boun...@brainvis.wustl.edu<mailto:caret-users-boun...@brainvis.wustl.edu>] on behalf of Timothy Coalson [tsc...@mst.edu<mailto:tsc...@mst.edu>] Sent: Wednesday, August 06, 2014 1:27 PM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Correction, there is a matlab GIFTI toolbox, not CIFTI. Metric files are usually already GIFTI files, but caret5 coord/topo files need to be converted: to convert non-GIFTI metric file to GIFTI: caret_command -file-convert -format-convert XML_BASE64_GZIP <file> to convert topo/coord to GIFTI surface: caret_command -file-conver -sc -is CARET <coord> <topo> -os GS <something.surf.gii> I believe the matlab GIFTI toolbox will read surface files, but you'll need to separate the two data arrays in it as to which describes the triangles, and which is the vertex coordinates. Tim On Wed, Aug 6, 2014 at 8:32 AM, Donna Dierker <do...@brainvis.wustl.edu<mailto:do...@brainvis.wustl.edu>> wrote: First, I want to point out that there is a CIFTI matlab toolkit, I think, but I know very little about it (or matlab in general). What I do know: * The freesurfer_to_fs_LR pipeline probably doesn't generate CIFTI output. But the forthcoming Human Connectome Project (HCP) pipeline does. * Questions about the CIFTI matlab toolkit might better be posed to the CIFTI forum on nitrc.org<http://nitrc.org> (http://www.nitrc.org/forum/?group_id=454). Using the caret5/caret_command tools, it is possible to convert the metric/func.gii files to ASCII, e.g.: caret_command -file-convert -format-convert ASCII my_fmri.metric … or: caret_command -file-convert -format-convert ASCII my_fmri.func.gii As for the coordinates, since you have the individual midthickness surfaces on 164k mesh, you can those for the unprojection command. If you really want a grid, then it is a border file you will get out of caret: http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#borderFile Here is the Alex Cohen paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705206/ This is not a trivial task. ;-) On Aug 5, 2014, at 3:13 PM, "Tang, Yan" <yan.t...@ttu.edu<mailto:yan.t...@ttu.edu>> wrote: > 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<mailto:caret-users-boun...@brainvis.wustl.edu> > > [caret-users-boun...@brainvis.wustl.edu<mailto:caret-users-boun...@brainvis.wustl.edu>] > on behalf of Donna Dierker > [do...@brainvis.wustl.edu<mailto: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<mailto: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<mailto:caret-users-boun...@brainvis.wustl.edu> >> >> [caret-users-boun...@brainvis.wustl.edu<mailto:caret-users-boun...@brainvis.wustl.edu>] >> on behalf of Donna Dierker >> [donna.dier...@sbcglobal.net<mailto: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<mailto: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<mailto:caret-users-boun...@brainvis.wustl.edu> >>> >>> [caret-users-boun...@brainvis.wustl.edu<mailto:caret-users-boun...@brainvis.wustl.edu>] >>> on behalf of Donna Dierker >>> [donna.dier...@sbcglobal.net<mailto: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<mailto: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<mailto:caret-users-boun...@brainvis.wustl.edu> >>>> >>>> [caret-users-boun...@brainvis.wustl.edu<mailto:caret-users-boun...@brainvis.wustl.edu>] >>>> on behalf of Donna Dierker >>>> [donna.dier...@sbcglobal.net<mailto: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<mailto: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<mailto:caret-users@brainvis.wustl.edu> >>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> caret-users@brainvis.wustl.edu<mailto:caret-users@brainvis.wustl.edu> >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> caret-users@brainvis.wustl.edu<mailto:caret-users@brainvis.wustl.edu> >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu<mailto:caret-users@brainvis.wustl.edu> >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> <QQ截图20140801162715.png>_______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu<mailto:caret-users@brainvis.wustl.edu> >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu<mailto:caret-users@brainvis.wustl.edu> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu<mailto:caret-users@brainvis.wustl.edu> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu<mailto:caret-users@brainvis.wustl.edu> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu<mailto:caret-users@brainvis.wustl.edu> > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu<mailto:caret-users@brainvis.wustl.edu> http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu<mailto:caret-users@brainvis.wustl.edu> http://brainvis.wustl.edu/mailman/listinfo/caret-users
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