I am sorry that I still don't know how to do it. Firstly, regularly spaced Cartesian grids were generated on the flattened PALS-B12 average surface of the left and right hemispheres using the Caret software. Grid points were spaced 20 mm apart on the flattened surface. Then, How to get the 3-dimensional (3D) stereotactic coordinates? Need I save this grid as a file and read this file? But how to save it? the coordinates I can get is the MNI coordinates?
From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [do...@brainvis.wustl.edu] Sent: Wednesday, August 06, 2014 8:32 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces 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://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> 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 > [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 >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> <QQ截图20140801162715.png>_______________________________________________ >>> 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 _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
