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-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [tsc...@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.t...@ttu.edu<mailto:yan.t...@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-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 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.t...@ttu.edu<mailto:yan.t...@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-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
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