A foci file from Caret5 cannot be imported into wb_view but one can convert the foci file to a foci projection file and import the foci projection file.
In Caret5: * Load your foci file and the surface(s) on which you created your foci. * Select Layers Menu->Foci->Project Fiducial Foci * In the Foci Projection dialog Data For Projection: select All (no sign flips to match hemisphere). Press the OK button * Select File Menu->Save Data File. Set the File Type to Foci Projection Files and possibly change the name of file. Press Save. wb_import: * Run wb_import using the foci projection file saved in the previous steps. As a technical note, a foci file places each focus at a stereotaxic coordinate (X, Y, Z). Foci in stereotaxic coordinates are only viewable on the anatomical surface (we used the term fiducial surface in Caret5). A foci projection file attaches each focus to three surface vertices using barycentric coordinates. The use of barycentric coordinates allows viewing of foci on other surface types (inflated, spherical, and others). John Harwell > On Dec 23, 2015, at 12:52 AM, #LONG HONGQUAN# <[email protected]> wrote: > > Hi David and Tim, > > Thank you for your help! I have tried to create .foci manually on the wb_view > and it looks great. > > Also, as you suggested, I am trying to use Caret with greater capabilities > but have encountered another problem. > > After I created a .foci file using Caret, I am not able to import it for > wb_view with the following ERROR: > > $ ./workbench/bin_macosx64/wb_import -data-file Neuron_consensus_264.foci > ERROR CONVERTING Neuron_consensus_264.foci: Conversion of FociFile not > implemented. > > I am using MAC OSX environment and the latest workbench version (1.1.1). Is > it because of the incompleteness of the package? Or I have used an invalid > instruction? > > There is another question. I am trying to extract time series from > Preprocessed Resting State MRI subjects in HCP Database. Can anyone tell me > what are the exact differences among the following four rfMRI scans? > > rfMRI_REST1_LR > rfMRI_REST1_RL > rfMRI_REST2_LR > rfMRI_REST2_RL > > Are they independent scans with the same coordinate? What is the exact > difference between REST1 session and REST2 session? What is the difference > between LR and RL(since both contain information of the whole brain)? > > Thank you a lot for your patience and help. It has been really helpful for me > as an undergraduate CS student learning a new field. > > Best Regards, > Hongquan > >> On 9 Dec 2015, at 10:26 AM, David Van Essen <[email protected] >> <mailto:[email protected]>> wrote: >> >> Hi Hongquan, >> >> Based on your description, I think foci files may be the best fit for your >> needs. Tim is correct that foci have to date been more extensively used in >> Caret than in Workbench and that there aren’t yet a lot of wb_command tools >> for manipulating foci (but there are a few listed in wb_command >> -list-commands). >> >> Foci can be generated in wb_view using options available in Toolbar: Mode: >> Foci, and their display can be controlled in Features Toolbox: Foci >> >> Foci can be viewed in relation to volume slices as well as surfaces. >> >> Also, if you decide to start by working with foci using the (currently) >> greater capabilities in Caret software, they can be imported for wb_view >> visualization using wb_import >> >> If you have specific questions as you proceed, please post them to >> hcp-users. Likewise we welcome specific feature requests, as Workbench is >> under ongoing development. (Indeed, we plan a new release this winter, with >> some very handy ‘annotation’ capabilities for adding text and symbols and >> saving them in scene files.) >> >> David VE >> >> >>> On Dec 8, 2015, at 5:13 PM, Timothy Coalson <[email protected] >>> <mailto:[email protected]>> wrote: >>> >>> Consider this command: >>> >>> http://www.humanconnectome.org/software/workbench-command.php?function=-surface-closest-vertex >>> >>> <http://www.humanconnectome.org/software/workbench-command.php?function=-surface-closest-vertex> >>> >>> You can draw ROIs around the identified vertices on the surface with this >>> command: >>> >>> http://www.humanconnectome.org/software/workbench-command.php?function=-surface-geodesic-rois >>> >>> <http://www.humanconnectome.org/software/workbench-command.php?function=-surface-geodesic-rois> >>> >>> You could then use -metric-reduce to make them into a single column, and >>> then either use different palettes or palette settings on the right and >>> left to color them differently, or turn them into label files to set their >>> colors directly. >>> >>> Subcortical points are more difficult, but you can use the "volume" mode in >>> wb_view to edit voxels in a new volume file. You can then use >>> -volume-dilate to make them more sphere-like, then display them with the >>> surfaces and metrics in "all" view, press the wrench icon for the volume, >>> layer tab, "draw voxels as cubes (3D)" to see them all at once. >>> >>> There is also an older file format for foci, used in caret5, which is still >>> supported for display, but we don't have many commands for that file type >>> in workbench, so it may be more involved to get it to work. It displays >>> the foci as spheres by default, so it would likely look better than the >>> above method. I'm not sure how it deals with subcortical foci. >>> >>> Tim >>> >>> >>> On Tue, Dec 8, 2015 at 9:05 AM, #LONG HONGQUAN# <[email protected] >>> <mailto:[email protected]>> wrote: >>> Hi HCP team, >>> >>> I am new using HCP dataset and the workbench. I have been struggling for a >>> while for drawing points on the brain, and now I would like to seek for >>> help from experienced users. >>> >>> I have some points in MNI coordinates(XYZ, radius = 10mm, can be >>> transformed to IJK), some are cortical points and some are subcortical. I >>> have assigned those points to be different groups. >>> >>> I would like to draw those points on the brain (especially Cortex Left and >>> Cortex Right surface). And I want to show different colours for different >>> groups. >>> >>> Now what I can do is only click on the surface using wb_view. Is there a >>> way to show the dedicated points on a brain surface? >>> >>> I would really appreciate if anyone could clarify my doubts. >>> >>> Thank you a lot. >>> >>> Best Regards, >>> >>> >>> Hongquan >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] <mailto:[email protected]> >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] <mailto:[email protected]> >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
