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 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 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 _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
