I still have problem. How can I know which brain region is every vertex belonged to? ________________________________________ From: Tang, Yan Sent: Friday, August 15, 2014 12:27 PM To: Caret, SureFit, and SuMS software users Subject: RE: [caret-users] projecting functional MRI to gii surfaces
Thank all of you. Thank you very much. ________________________________________ 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 13, 2014 2:27 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] projecting functional MRI to gii surfaces 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.t...@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-boun...@brainvis.wustl.edu > [caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson > [tsc...@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.t...@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-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> 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 > [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker > [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> 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 > > [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 _______________________________________________ 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
