Hi Yan, There are lots of ways to split up the brain -- "parcellations". For example, the Conte69 atlas (http://brainvis.wustl.edu/wiki/index.php/Caret:Conte69_Atlas) comes with two label.gii files per hemisphere, e.g.:
parcellations_VGD11b.R.164k_fs_LR.label.gii RSN-networks.R.164k_fs_LR.label.gii The first includes two parcellations: Composite Parcellation-rh (FRB08_OFP03_retinotopic) Brodmann rh (from colin.R via pals_R-to-fs_LR) The second includes four parcellations: 7 RSN Networks (YKS11 - Yeo et al., JNP, 2011) 17 RSN Networks (YKS11 - Yeo et al., JNP, 2011) RSN consensus communities (holes filled) (PCN11 - Power_Neuron11) RSN consensus communities (PCN11 - Power_Neuron11) And lots more have been published since, and will continue to be published. ;-) So you have to decide which one you want. Then you can either load that parcellation in wb_view (or caret5) and click on nodes interactively, or if you want to write a script that queries regions, there is a lookup table that maps the label key to a label name in the front of the label file, e.g.: <Label Key="0" Red="0.667" Green="0.667" Blue="0.667" Alpha="0"><![CDATA[???]]></Label> <Label Key="1" Red="1" Green="1" Blue="1" Alpha="1"><![CDATA[u1_Unassigned]]></Label> <Label Key="2" Red="0.502" Green="0.502" Blue="0.502" Alpha="1"><![CDATA[u2_Ventral_frontal_temporal]]></Label> <Label Key="3" Red="1" Green="0" Blue="0" Alpha="1"><![CDATA[a3_Default_mode]]></Label> <Label Key="4" Red="0" Green="1" Blue="1" Alpha="1"><![CDATA[a4_"Hand"_somatosensory-motor]]></Label> <Label Key="5" Red="0" Green="0" Blue="1" Alpha="1"><![CDATA[a5_Visual]]></Label> <Label Key="6" Red="0.961" Green="0.961" Blue="0.059" Alpha="1"><![CDATA[a6_Fronto-parietal_task_control]]></Label> <Label Key="7" Red="0" Green="0.502" Blue="0.502" Alpha="1"><![CDATA[a7_Ventral_attention]]></Label> <Label Key="8" Red="0" Green="0.275" Blue="0.157" Alpha="1"><![CDATA[a8_Caudate_putamen]]></Label> <Label Key="9" Red="1" Green="0.722" Blue="0.831" Alpha="1"><![CDATA[a9_Superior_temporal_gyrus]]></Label> <Label Key="10" Red="0.675" Green="0.675" Blue="0.675" Alpha="1"><![CDATA[u10_Inferior_temporal_pole]]></Label> You can also export the label table as ASCII text. But each vertex is associated with one of these keys in the label.gii file. Donna On Aug 28, 2014, at 2:27 PM, "Tang, Yan" <yan.t...@ttu.edu> wrote: > 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 _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users