Re: [HCP-Users] Trouble with command line wb_view

Hi Michael, With the C-shell (csh) and T-shell (tcsh), you may need to use ’setenv’ instead of ’set’ in the ‘.cshrc’ file. Use ‘printenv’ to show the path. https://www.cyberciti.biz/faq/unix-linux-difference-between-set-and-setenv-c-shell-variable/ John Harwell On May 10, 2019, at 12:24 PM, M

Re: [HCP-Users] Surface Contrast and Overlay Transparency

Matt, I Caret5, there were controls for adjusting the brightness and contrast of a surface that were applied even if there were no overlays available for the surface. John On Mar 18, 2019, at 10:05 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: 1. I am not sure what you mean by

Re: [HCP-Users] Surface Contrast and Overlay Transparency

Hi Michael, On Mar 18, 2019, at 6:02 AM, Michael Riedel mailto:mirie...@fiu.edu>> wrote: I have two questions that are probably easy fixes, but I can’t seem to find the solution. First, is there a way to change the contrast of the surface renderings? I know Caret had this as an option in the

Re: [HCP-Users] Exporting dynconn layer for statistical analysis

Hello, You can export the data loaded (and displayed) from the dynconn file into a scalar file. * Click on a surface or volume to display data from the dynconn file. * Go to Overlay ToolBox—>Connectivity * Click the Copy button in the row containing the dynconn file. * Go to Overlay ToolBox—>La

Re: [HCP-Users] combining tabs from different scenes within a scene file

Merging scenes is not feasible. A scene contains the entire ‘internal state’ of wb_view. As you have observed, loading a second scene overwrites the first scene. In the future, you could try following these steps: * Load the data files required for all of your scenes * Setup Tab 1 for your fir

Re: [HCP-Users] wb_view error in structuralQC

Will wb_view start without loading a scene file? Which version of wb_view are you using (File Menu —> About wb_view)? How was the scene file created? In wb_view or by a script? If you upload your scene file at http://brainvis.wustl.edu/cgi-bin/upload.cgi, I can try to determine the cause of th

Re: [HCP-Users] drawing borders

lto:demian.wasserm...@inria.fr> Associate Research Professor (CRN) Parietal Lab INRIA Saclay Ile-de-France 1 Rue Honoré d'Estienne d'Orves, 91120 Palaiseau On 10 Oct 2018, at 10:51, Harwell, John mailto:jharw...@wustl.edu>> wrote: There is nothing in the user interface to adjust the

Re: [HCP-Users] drawing borders

h the same surface? > > gaurav patel > gauravpa...@gmail.com > pateldsclab.net > >> On Oct 10, 2018, at 9:50 AM, Harwell, John wrote: >> >> There is nothing in the user interface to adjust the size of the spheres >> while drawing a border. In a prev

Re: [HCP-Users] drawing borders

lab.net<http://pateldsclab.net/> On Oct 9, 2018, at 1:07 PM, Harwell, John mailto:jharw...@wustl.edu>> wrote: How huge is huge? When drawing a new border, the symbol size should be about 3% of the longest surface axis. On a human surface, that appears be about 5mm. There is no way fo

Re: [HCP-Users] drawing borders

How huge is huge? When drawing a new border, the symbol size should be about 3% of the longest surface axis. On a human surface, that appears be about 5mm. There is no way for the user to adjust the symbol size when drawing. I am using Workbench version 1.3.2 and the size should be the same i

Re: [HCP-Users] Locating a seed for functional connectivity

Hello, You may be able to use wb_command to convert a list of surface coordinates into a list of surface vertex indices. wb_command is included with Connectome Workbench and must be run from within a terminal window (Command Prompt). “wb_command -surface-closest-vertex” accepts as input a G

Re: [HCP-Users] -show-scene windows

Hi Garren, Unfortunately, we have never been able to get the “-show-scene” command to function on Windows. It is available in the Mac and Linux versions of wb_command. John Harwell On Jul 22, 2018, at 1:16 PM, Garren Gaut mailto:gbiu...@gmail.com>> wrote: Hi HCP, I recently downloaded the

Re: [HCP-Users] MMP labels and mesh modification

There may be some confusion between annotations and labels. Annotations are the text characters on the surface that identify the parcels (e.g.: “MST”). Labels refer to the data file overlayed on the surface that colors brainordinates (surface vertices) by associating a color with a name. The

Re: [HCP-Users] Gifti files in HCP - conversion to VTK

Workbench does not transform the GIFTI Surface Files. Workbench draws volumes in coordinate space (not voxel IJK space) using the NIFTI ‘sform’ or ‘qform’. If the software you are using ignores the NIFTI ‘sform’ or ‘qform’ that may be why the data does not align. ‘wb_command -file-informati

Re: [HCP-Users] Human-Macaque deformation map in wb_view?

bdi mailto:saad.jba...@ndcn.ox.ac.uk>> wrote: This one On 12 Apr 2018, at 15:21, Harwell, John mailto:jharw...@wustl.edu>> wrote: Do you know the name and type of the file displayed as the primary overlay on the surface? It should be selected in Primary Overlay on the Display Control’s O

Re: [HCP-Users] Human-Macaque deformation map in wb_view?

t;1.0" NumberOfDataArrays="0"> On 11 Apr 2018, at 19:24, Harwell, John mailto:jharw.

Re: [HCP-Users] Human-Macaque deformation map in wb_view?

In Caret5: * Select File Menu -> Save Data File * In the Save Data File Dialog, set the File Type to GIFTI Functional File (*.func.gii) * Change the File Name so that it ends in “.func.gii” (may want to click the File Name button to choose the name with a file selection dialog) * Verify that the

Re: [HCP-Users] Problem creating scenes in wb_view

This error has been reported before (WB-647 in our internal bug tracking system). The solution for the user that experienced this problem was to use the version of Workbench distributed through the HCP website (https://www.humanconnectome.org/software/get-connectome-workbench). From some googl

Re: [HCP-Users] wb_view crashes after 1 day of using it

Hello, Is wb_view crashing when loading a file or when you are performing an operation, perhaps editing annotations? John > On Feb 23, 2018, at 12:20 PM, Marta Moreno wrote: > > Dear experts, > > My wb_view crashes after 1 day of using it, what happens is that the next day > I cannot keep l

Re: [HCP-Users] gif surface to obj

Hello, No. Connectome Workbench is unable to convert GIFTI files to OBJ files. John Harwell On Feb 21, 2018, at 10:18 AM, Shadi, Kamal mailto:kamal.shad...@gatech.edu>> wrote: Hi all, Does human connectome workbench have a tool to convert gii surfaces to obj? Thanks, Kamal

Re: [HCP-Users] Drawing borders on connectome workbench

Changes were made to allow pan/zoom/rotation of the surface while in border drawing mode. In addition, use of the ALT was removed as a particular operating systems grabbed the ALT key and used it for other purposes. If you place the mouse over the “New” button in the border toolbar, a tooltip

Re: [HCP-Users] Connectome Workbench Config File

Hello, If you are on a Linux system, try setting the environment variable XDG_CONFIG_HOME for each user to a shared directory (search for XDG_CONFIG_HOME in http://doc.qt.io/qt-5/qsettings.html). This should result in a new config file path (./brainvis.wustl.edu/Caret7.conf

Re: [HCP-Users] workbench crashes - Namespace SIGNAL, Code 0xb

Is wb_view crashing with any file or with specific files? Can I get a copy of a file that is causing the crash? John Harwell > On Dec 26, 2017, at 2:20 PM, Marta Moreno wrote: > > Thanks. > > What details do you need to help? > > It crashes anytime I try to open a new file. I am running ma

Re: [HCP-Users] error open file in wb_view

as the MATLAB_R2017b. On Dec 12, 2017, at 1:12 PM, Harwell, John mailto:jharw...@wustl.edu>> wrote: Hi Marta, Does wb_view start up if you do not try to load any files? Is this the first time you have run wb_view on this Mac? Do you know which file is causing the crash? You could u

Re: [HCP-Users] error open file in wb_view

Hi Marta, Does wb_view start up if you do not try to load any files? Is this the first time you have run wb_view on this Mac? Do you know which file is causing the crash? You could use File Menu —> Open File and try opening just a surface file. John Harwell > On Dec 12, 2017, at 11

Re: [HCP-Users] RGBA files in connectome workbench

Hi Corina, At this time, Connectome Workbench is not able to display RGBA files. I do not know when, or if, display of RGBA files will be added. As Matt Glasser indicated in his response, you may want to try using a Label file. A label file contains integers where each value is an index into

Re: [HCP-Users] wb_shortcuts dyld: lazy symbol binding error

Tim and Kelly, This error probably occurs when wb_shortcuts runs ‘mris-convert’. A solution for the “lazy symbol” errors is described at the end of these FreeSurfer Release Notes: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes If your FreeSurfer installation is up to date, the release

Re: [HCP-Users] Open files in wb_view via script

Keren, wb_view accepts multiple files when run from the command line (wb_view -help). If you run “wb_view file_1.nii file_2.nii file_3.nii” you should have one instance of wb_view with the three files loaded. John Harwell On Sep 28, 2017, at 7:52 AM, Keren Kotler mailto:kerenkotl...@gm

Re: [HCP-Users] Neigbours about a vertex

The surface files are in GIFTI format and documentation for the GIFTI format is available at https://www.nitrc.org/projects/gifti. GIFTI files support several formats including ASCII (text) that can be viewed in a text editor. A GIFTI file is converted to ASCII format using Connectome Workbenc

Re: [HCP-Users] removing cross-hairs, slice labels when using wb_command -show-scene?

Hi Keith, The settings for volume cross-hairs and slice labels are only in the preferences file; they are not in the scene file. Both wb_view and wb_command use the same preferences so as long as you are on the same computer and do not change the status of crosshairs/labels, their appearance s

Re: [HCP-Users] wb_view : Image Capture Problems

There is an option for changing the way images are captured: * Display the Preferences Dialog by selecting File Menu->Preferences. * On the Preferences Dialog, click the OpenGL tab. * Change Image Capture Method to Grab Frame Buffer. * Close the Preferences Dialog and try image capture again. It a

Re: [HCP-Users] Making a movie in connectome workbench

Hello Kristian, * Load your files into Workbench and select the first map in your GIFTI file. * Select File Menu->Animation Control. * On the Animation Control Dialog, press the Record button (near the top right of the dialog). * In the Workbench window, click the mouse in the map index control

Re: [HCP-Users] Edit colors of palette in wb view?

ld you recommend? Thank you very much, Xavier. From: hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> [hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>] on behalf of Harwell, John [

[HCP-Users] Edit colors of palette in wb view?

Hello, You will need to convert your data to the CIFTI Label File format using “wb_command". A label table contains a group of labels and each label consists of a text name, RGB color components, and an integer value. When the data is displayed, coloring is performed by matching data values t

[HCP-Users] Solution for: Continuous border drawing holding "alt/option" key does not work

Question: I am using wb_view version 1.2.3. I have noticed that it is not possible to draw a continuous line by holding down the alt/option key and the left mouse button while dragging the mouse. Drawing a border is possible only by drawing multiple points. Is this a known issue, or am I doing

Re: [HCP-Users] wb_view could not capture the image

For the user experiencing a crash during image capture on Linux: There are a couple of things you can try: * The (File Menu —-> Preferences) Preferences Dialog’s OpenGL tab contains a selection for “Image Capture Method”. Change the selection for image capture and see if wb_view still crashes.