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

[Harwell, John]

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, Michael Amlung 
mailto:michael.aml...@gmail.com>> wrote:

I cannot get the command line tools to work for wb_view on Mac.
> wb_view
wb_view: Command not found.

I have tried everything in the README.txt file, including adding the line to 
the path.

I confirmed that my .cshrc looks like this:
set PATH = ($PATH /Applications/workbench/bin_macosx64/)

when I print the PATH, I see /Applications/workbench/bin_macosx64

I confirmed I am running /bin/tcsh

But for some reason it cannot locate the wb_view command. The program opens 
fine if I open it form the LaunchPad.

Any suggestions?


Michael Amlung, Ph.D.

Email: michael.aml...@gmail.com



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

[Harwell, John]

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 visualizer under “Surface Miscellaneous", 
but I can’t find it in wb_view or any of the associated command line tools.

To adjust the surface contrast, you will need some type of data, such as 
curvature on the surface.  If you have such data, its colorization is adjusted 
in the same manner as your func.giii. file.

Second, Ive created a .func.gii by converting a NIFTI using 
-volume-to-surface-mapping (and one of the tutorial surfaces) and slightly 
edited using -metric-palette. When I overlay this metric onto a surface and try 
to change the transparency, the more transparent (closer to 0) I set the 
threshold, the more black the overlay becomes, and its completely black with a 
transparency of 0. Am I missing a step or need to set my thresholds differently 
in the metric palette (than default)?

Your func.gii file should be listed in the Overlay ToolBox at the bottom of the 
window.  If you press the ‘wrench’ button in the row containing your file, the 
Overlay and Map Settings dialog is displayed. On this dialog there are controls 
for both thresholding and mapping your data to a color palette.  Try 
thresholding instead of opacity.  For more information on this dialog, select 
Help Menu —> Workbench Help.  In the Help dialog, click the Search Tab and 
scroll down to Overlay and Map Settings.


Any help would be appreciated!

Michael

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

[Harwell, John]

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—>Layers
* Click one of the ComboBoxes under File and there should be a new item with a 
name similar to 
“CP10101_HCP_Pilot-1.fMRI.dynconn_Row_14906_Vertex_Index_16615_Structure_CortexLeft.dscalar.nii”.
* Select File Menu—>Save/Manage Files
* There should be a CIFTI-Dense Scalar file with a “Yes” modified status (in 
red letters)
* If you want to change the name of the file click the sprocket icon in the 
More column and select Set File Name.
* Press the Save Checked Files button to save the file

John Harwell


On Feb 20, 2019, at 10:47 AM, Jayasekera, Dinal 
mailto:dinal.jayasek...@wustl.edu>> wrote:

Dear all,

I have processed some patient data through the dedrift pipeline and I've been 
been using wb_view to look at the 
${fMRIConcatName}_Atlas_MSMAll_hp0_clean.dtseries.nii file along with using the 
.dynconn layer to do point and click functional connectivity.

Is it possible to export the file after placing a point on this .dynconn layer 
for statistical comparison with other patients who have a point placed at the 
same location?


Kind regards,
Dinal Jayasekera

PhD Candidate | InSITE Fellow
Ammar Hawasli Lab
Department of Biomedical Engineering 
| Washington University in St. Louis

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

[Harwell, John]

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 first scene and create your first scene
* Add a new tab, Tab 2, setup Tab 2 for your second scene, and add (create) 
your second scene
* Add and setup additional tabs for scenes
* After all tabs have been created, enable Tile Tabs

John Harwell

On Dec 14, 2018, at 9:18 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

Hi Ely,

Unfortunately this is not supported.  I don’t know if it would be feasible to 
support or not either.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Ely, Benjamin" 
mailto:benjamin@mssm.edu>>
Date: Friday, December 14, 2018 at 9:01 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] combining tabs from different scenes within a scene file

Hi all,

I currently have a scene file where I created a separate scene for each panel 
of a figure. I'd like to combine the tabs from these scenes into a single scene 
and display them using the tile tab feature. Is there a way to do this? 
Whenever I load a second scene, it closes all tabs associated with the first 
scene. I've tried opening a new window and then loading the second scene, but 
it just closes the second window and loads the scene into the first window. 
I've also tried opening a second instance of Workbench Viewer, which 
successfully displays the second scene, but there doesn't seem to be a way to 
move tabs from one instance to another. I'm using wb version 1.3.2 on Mac.

Thank you!
-Ely
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Re: [HCP-Users] wb_view error in structuralQC

[Harwell, John]

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 the problem.

John Harwell

On Nov 15, 2018, at 10:14 AM, Moataz Assem 
mailto:moataz.as...@mrc-cbu.cam.ac.uk>> wrote:

Hi,

We ran the structural QC 
(https://github.com/Washington-University/StructuralQC) on our data but when 
loading a scene we get the following error:

/Software/workbench-rh_linux64-v1.3.0/workbench/bin_rh_linux64/wb_view: line 
17: 171498 Segmentation fault  "$directory"/../exe_rh_linux64/wb_view "$@"

Any idea why we might be getting this error?

Thanks

Moataz

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Re: [HCP-Users] drawing borders

[Harwell, John]

Borders are not annotations and that is why borders are not in the annotations 
guide.  Borders are always attached to a surface whereas annotations may or may 
not be attached to a surface.  Visualizing borders is covered in the Workbench 
1.0 - 1.3.2 Tutorial 
(https://www.humanconnectome.org/software/connectome-workbench).  There is a 
description in the Workbench Help for border drawing (Help Menu—> Workbench 
Help), look for “Toolbar -> Mode -> Border Drawing.   Borders are simply a 
sequence of points that may be closed, it just depends upon how the border is 
drawn.

On Oct 10, 2018, at 10:01 AM, Demian Wassermann 
mailto:demian.wasserm...@inria.fr>> wrote:

This is an interesting topic. Despite the 3% being a good idea the border 
depends more on the structure being traced than on the brain itself (arguably 
those two are also related). I haven’t managed to find border tracing on the 
tutorial of annotations. Am I looking on the wrong place? Also are the 
traceable borders closed curves or can be also simple curves? Ie lines instead 
of borders?

Best and thanks for all this work


Demian

--
Demian Wassermann, PhD
demian.wasserm...@inria.fr<mailto: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 size of the spheres while 
drawing a border.  In a previous version of Workbench, the size was 2mm.  
However, 2mm was far too large when drawing borders on very small brains 
(babies, mice, etc) so the size was changed to 3% of the longest surface axis 
(typically posterior-to-anterior).

John

On Oct 9, 2018, at 12:58 PM, Gaurav Patel 
mailto:gauravpa...@gmail.com>> wrote:

here’s a screen shot of the draw borders output vs. a finished border (symbol 
diameter set to 2mm).  I tried to change the ID sphere size property, and that 
did not change.  On a machine with 1.23 still installed, the draw borders 
output is the same size as the 2mm diameter finalized borders.  I am drawing 
this on the tutorial surface



 gaurav patel
 gauravpa...@gmail.com<mailto:gauravpa...@gmail.com>
 pateldsclab.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 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 in 1.3.1.

John Harwell

On Oct 9, 2018, at 11:37 AM, Gaurav Patel 
mailto:gauravpa...@gmail.com>> wrote:

Hi—when I am drawing borders in wb_view 1.31, the diameters of the red spheres 
is huge, making is difficult to see what I am drawing.  This was not the case 
in 1.23.  Is there a way to change that setting?  Finishing the border reduces 
the size of the spheres to the setting in the borders menu, so that setting 
doesn’t make a difference.  Thanks

gaurav patel
gauravpa...@gmail.com<mailto:gauravpa...@gmail.com>
pateldsclab.net<http://pateldsclab.net/>


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Re: [HCP-Users] drawing borders

[Harwell, John]

When drawing a border, I am able to reproduce the border sizes displayed in 
your image.  I would describe the border symbols as a little bigger, but not 
huge.  We understand this is not optimal for you, but there is nothing we can 
do to immediately change the border drawing symbol size.

> On Oct 10, 2018, at 9:57 AM, Gaurav Patel  wrote:
> 
> this is the tutorial 1.0 brain 
> (Q1-Q6_R440.R.veryinflated.32k_fs_LR.surf.gii).  2mm was actually much 
> smaller than the current 3% standard for the adult brain.  Are you able to 
> reproduce the issue with 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 previous version of Workbench, the size was 
>> 2mm.  However, 2mm was far too large when drawing borders on very small 
>> brains (babies, mice, etc) so the size was changed to 3% of the longest 
>> surface axis (typically posterior-to-anterior).
>> 
>> John
>> 
>>> On Oct 9, 2018, at 12:58 PM, Gaurav Patel  wrote:
>>> 
>>> here’s a screen shot of the draw borders output vs. a finished border 
>>> (symbol diameter set to 2mm).  I tried to change the ID sphere size 
>>> property, and that did not change.  On a machine with 1.23 still installed, 
>>> the draw borders output is the same size as the 2mm diameter finalized 
>>> borders.  I am drawing this on the tutorial surface
>>> 
>>> 
>>> 
>>> gaurav patel
>>> gauravpa...@gmail.com
>>> pateldsclab.net
>>> 
>>>> On Oct 9, 2018, at 1:07 PM, Harwell, John  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 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 in 
>>>> 1.3.1.
>>>> 
>>>> John Harwell
>>>> 
>>>>> On Oct 9, 2018, at 11:37 AM, Gaurav Patel  wrote:
>>>>> 
>>>>> Hi—when I am drawing borders in wb_view 1.31, the diameters of the red 
>>>>> spheres is huge, making is difficult to see what I am drawing.  This was 
>>>>> not the case in 1.23.  Is there a way to change that setting?  Finishing 
>>>>> the border reduces the size of the spheres to the setting in the borders 
>>>>> menu, so that setting doesn’t make a difference.  Thanks
>>>>> 
>>>>> gaurav patel
>>>>> gauravpa...@gmail.com
>>>>> pateldsclab.net
>>>>> 
>>>>> 
>>>>> ___
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>>>>> HCP-Users@humanconnectome.org
>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>> 
>>> 
>> 
> 


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Re: [HCP-Users] drawing borders

[Harwell, John]

There is nothing in the user interface to adjust the size of the spheres while 
drawing a border.  In a previous version of Workbench, the size was 2mm.  
However, 2mm was far too large when drawing borders on very small brains 
(babies, mice, etc) so the size was changed to 3% of the longest surface axis 
(typically posterior-to-anterior).

John

On Oct 9, 2018, at 12:58 PM, Gaurav Patel 
mailto:gauravpa...@gmail.com>> wrote:

here’s a screen shot of the draw borders output vs. a finished border (symbol 
diameter set to 2mm).  I tried to change the ID sphere size property, and that 
did not change.  On a machine with 1.23 still installed, the draw borders 
output is the same size as the 2mm diameter finalized borders.  I am drawing 
this on the tutorial surface



 gaurav patel
 gauravpa...@gmail.com<mailto:gauravpa...@gmail.com>
 pateldsclab.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 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 in 1.3.1.

John Harwell

On Oct 9, 2018, at 11:37 AM, Gaurav Patel 
mailto:gauravpa...@gmail.com>> wrote:

Hi—when I am drawing borders in wb_view 1.31, the diameters of the red spheres 
is huge, making is difficult to see what I am drawing.  This was not the case 
in 1.23.  Is there a way to change that setting?  Finishing the border reduces 
the size of the spheres to the setting in the borders menu, so that setting 
doesn’t make a difference.  Thanks

gaurav patel
gauravpa...@gmail.com<mailto:gauravpa...@gmail.com>
pateldsclab.net<http://pateldsclab.net>


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

[Harwell, John]

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 GIFTI surface file 
and a text file containing XYZ coordinates.  The output is a text file 
containing the indices of the vertices nearest the coordinates.  If you are 
using MNI coordinates, the surface must be an anatomical surface that is in MNI 
stereotaxic space.

Once you have a list of vertex indices, return to Connectome Workbench.  Select 
Window Menu->Identify.  In the Identify Brainordinate Dialog, select Identify 
Surface Vertex, choose the Structure (Cortex Left or Cortex Right), enter a 
Vertex Index (from the output of wb_command -surface-closest-vertex), and press 
the Apply Button.  If there is connectivity data corresponding to the vertex, 
connectivity data is loaded.   Repeat for each vertex index.

Note that “wb_command  -surface-vertex” finds the “closest vertex" and it may 
be a long distance from the coordinate that you provide.  Each time the Apply 
button is clicked in the Identify Brainordinate Dialog, the Information Window 
will contain the 3D coordinate corresponding to the vertex index and it should 
be compared to the coordinate provided as input to “wb_command 
-surface-vertex”.  An identification symbol is also placed on the surface and 
should be inspected to verify that it is the correct anatomical location.



wb_command -surface-closest-vertex

FIND CLOSEST SURFACE VERTEX TO COORDINATES
   wb_command -surface-closest-vertex
   - the surface to use
   - text file with coordinates
   - output - the output text file with vertex numbers

  For each coordinate XYZ triple, find the closest vertex in the surface,
  and output its vertex number into a text file.  The input file should
  only use whitespace to separate coordinates (spaces, newlines, tabs), for
  instance:

  20 30 25
  30 -20 10




John Harwell



On Aug 14, 2018, at 8:38 AM, Kwan-Jin Jung 
mailto:kjj...@umass.edu>> wrote:

Hi,

Is there a way to define the seed location, i.e., MNI coordinate, on the cortex 
 in wb_view for the functional connectivity?
At this time, I input the coordinate into the Volume tab and I iteratively find 
a similar coordinate on the surface.
But it is tedious and difficult.

Kwan-Jin Jung, Ph.D.
UMASS Amherst

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

[Harwell, John]

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 workbench software for windows and am trying to use 
the -show-scene command, which seems to be missing. I get the following error:

wb_command -show-scene

While running:
C:\workbench\bin_windows64\wb_command.exe -show-scene

ERROR: the switch '-show-scene' does not match any processing commands


nor is the command -show-scene listed when I run:

wb_command -list-commands


-scene-file-mergeREARRANGE SCENES INTO A NEW FILE
-scene-file-relocate RECREATE SCENE FILE IN NEW LOCATION
-set-map-names   SET THE NAME OF ONE OR MORE MAPS IN A 
FILE
-set-structure   SET STRUCTURE OF A DATA FILE
-signed-distance-to-surface  COMPUTE SIGNED DISTANCE FROM ONE 
SURFACE TO ANOTHER
-spec-file-merge MERGE TWO SPEC FILES INTO ONE

...


nor is it on the list of deprecated commands:

$ wb_command -list-deprecated-commands
-cifti-change-timestepDEPRECATED: use -cifti-change-mapping
-cifti-convert-to-scalar  DEPRECATED: use -cifti-change-mapping
-cifti-copy-mapping   DEPRECATED: use -cifti-change-mapping
-cifti-separate-all   DEPRECATED: use -cifti-separate
-metric-vertex-sumDEPRECATED: use -metric-stats or 
-metric-weighted-stats
-set-map-name DEPRECATED: use -set-map-names


I am using the following version:

$ wb_command
Version: 1.3.1
Commit Date: 2018-06-04 20:08:38 -0500
Operating System: Windows

...


Has anyone else run into this problem? Any help would be greatly appreciated. 
Thank you!

-Garren

​

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

[Harwell, John]

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 annotations are contained in the scene and not in a separate data file.

If you want to disable the display of particular annotations:
* Display the features toolbox by clicking the toolbox icon on the far right 
side of the toolbar or View Menu -> Features Toolbox -> Attach to Right.
* In the Features ToolBox, click the Annot tab
* In the Main Window, click the tab for the surface that contains annotations 
that you want to hide.  A box will briefly appear around the surface when the 
tab is clicked.
* Return to the Features Toolbox.  Find the name of annotation you want to hide 
and uncheck the box next to the name.

In the features toolbox, there is a “Group” selection that allows one to 
control the display of annotations within a “Group”.  Each annotation contains 
a separate display status for each Group.  For this scene, you will see several 
annotations with the same name but each is displayed in only one group.  The 
reason is that on each surface (left, right, left flat, and right flat) the 
annotation needs a unique surface coordinate location.

To save your changes:
* Display the Scene Dialog by selecting the Clapboard icon in the Toolbar or 
Window Menu -> Scenes.
* Click the New button to create a new Scene File.
* Click the Add button to create a new scene and enter a name.
* Click the Save As button, enter the path and name for the scene file, click 
the File Dialog’s Save button to save the scene file.

For more information about annotations, select Help Menu -> Workbench Help.  In 
the Help Dialog, click on Annotations 1.3 (7th item from top in Table of 
Contents).


John Harwell


On May 24, 2018, at 2:30 AM, Amin Dadashi 
> wrote:

Thank you Tim. I could use your help to solve the second issue. However, In the 
first case, by turning the labels off their name do not disappear (the names on 
the list are even slightly different from the ones that are shown) . It seems 
to me that the ROI names are saved in a separate surface file and are shown as 
an overlay and it is not possible to remove them individually. There are so 
many files associated with this specific *.scene file and I could not figure 
out where to find the one that contains the ROIs name. I would appreciate if 
anyone could give me a hint.

On Thu, May 24, 2018, 03:37 Timothy Coalson 
> wrote:
1) Open the features toolbox (rightmost button near the top right of the 
window), select the "labels" tab, expand the list for the file in question, and 
uncheck the labels you don't want (you can use the checkbox on the file to 
start with them all turned off).

2) The command required is "wb_command -label-resample", use the 32k and 59k 
standard spheres (L.sphere... and R.sphere..., for the separate hemispheres) in 
the HCP Pipelines global/templates/standard_mesh_atlases folder.  The ideal way 
is to use ADAP_BARY_AREA, using 
global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR.?.midthickness.va_avg...
 in the -area-metrics option, but since this specific case is an upsampling, 
this may only have marginal improvements over using BARYCENTRIC (which doesn't 
need vertex area data).

Tim


On Wed, May 23, 2018 at 3:45 AM, Amin Dadashi 
> wrote:
Hello,

I am using "Glasser_et_al_2016_HCP_MMP1.0_6_AllAreasMap.scene" file of 
Multimodal Parcellation to localize the connectivity pattern of my study. I am 
using the 7T(1.6mm) HCP surface fMRI dataset. Now I have the following 
questions:

1. Is there any way to modify the shown parcellation labels of the "All Areas 
Map" scene file in wb_view? I want to delete the ones which are not relevant to 
my study.

2. How can I resample the "All Areas Map" labels and borders so I can overlay 
them on my 7T connectivity maps (59k mesh surface)?

Thank you,
Amin

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

[Harwell, John]

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-information  ’ will list the coordinate range for 
both a GIFTI surface file and a NIFTI volume file.

John

> On Apr 12, 2018, at 9:59 AM, Olivier Commowick  
> wrote:
> 
> Hi HCP users and moderators,
> 
> I have been trying lately to convert the gifti files from the preprocessed 
> data of HCP (in the Native folder) to the VTK format since there are tools we 
> use that are relying solely on this format. I have been encountering problems 
> though with the converted files that do not align properly with the image in 
> visualization softwares. To start with, I have tested two conversion methods: 
> one through matlab and SPM12, and one through the mris_convert tool of 
> freesurfer, both with the default parameters (no info on the T1 image 
> itself). In both cases, the result is the exact same i.e. a vtk surface that 
> does not align with the T1 image (with at least two flips on the X and Y axes 
> but probably not only).
> 
> What is weird to me though is that the gifti and T1 image align perfectly in 
> connectome workbench. This makes me think that either the software is doing 
> something specific to align them or is accounting for something in the gifti 
> file that I could not see. The only info I saw is that the gifti files are in 
> Talairach space (NIFTI_XFORM_TALAIRACH) and no orientation matrix is given 
> (identity). 
> 
> Would anyone know more about this ? Is workbench applying some transformation 
> on the fly to the gifti files when loading (in which case which one would be 
> helpful) ? Am I using the wrong files or am I missing something (and SPM and 
> freesurfer too) in the gifti files from HCP ?
> 
> Thanks a lot in advance
> 
> ---
> 
> Olivier Commowick, Ph.D.
> Research Scientist
> INRIA Rennes - Bretagne Atlantique, VISAGES Team
> Campus de Beaulieu
> 35042 Rennes
> FRANCE
> 
> Phone: +33 2 99 84 25 92
> Email: olivier.commow...@inria.fr
> Web: http://olivier.commowick.org/
> 
> 
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Re: [HCP-Users] Human-Macaque deformation map in wb_view?

[Harwell, John]

So it is a shape file.  Follow the same instructions as before except for the 
second step that has been updated to set the File Type to GIFTI Shape File.

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


Note that GIFTI func and shape are the same format and you can rename from 
.shape.gii to .func.gii.



Alternatively, if you can find the Caret Shape File in a terminal window, 
“wb_import”, included with the Workbench distribution, can be used to convert 
data files from Caret format to a Workbench compatible format.

wb_import -data-file
   CONVERT DATA FILE TO WORKBENCH FORMAT
  wb_import -data-file
 [-allow-overwrite]
 [-structure  structure-name]
 [-area-color-filearea-color-file-name]
 [-border-color-file  border-color-file-name]
 [-foci-color-filefoci-color-file-name]
 ]

On Apr 12, 2018, at 10:24 AM, Saad Jbabdi 
<saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

This one


On 12 Apr 2018, at 15:21, Harwell, John 
<jharw...@wustl.edu<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 
Overlay/Underlay - Surface page.


On Apr 12, 2018, at 7:41 AM, Saad Jbabdi 
<saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

Hi John

When I follow your steps it produces an empty func file:


http://www.nitrc.org/frs/download.php/1594/gifti.dtd;>
http://www.w3.org/2001/XMLSchema-instance;
  
xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd;
  Version="1.0"
  NumberOfDataArrays="0">
   
  
 
 
  
  
 
 
  
  
 
 
  
  
 
 
  
  
     
 
  
   
   




On 11 Apr 2018, at 19:24, Harwell, John 
<jharw...@wustl.edu<mailto:jharw...@wustl.edu>> wrote:

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 Encoding is XML.
* Click the Save button.

This should create a GIFTI functional file that can be loaded into wb_view.

John H

On Apr 11, 2018, at 12:47 PM, Saad Jbabdi 
<saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

Hi Matt

Thanks. But I am not sure I was clear enough so let me rephrase: is there a way 
to somehow export the attached map from Caret into a func.gi file that I can 
open in wb_view?

Thanks!
Saad



On 11 Apr 2018, at 16:36, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:

Hi Saad,

Not that I am aware of.  Probably better to generate distortion maps (e.g.
isotropic and anisotropic strains).

Matt.

On 4/11/18, 10:28 AM, 
"hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 on behalf of
Saad Jbabdi" 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 on behalf of
saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

Hi all,

Is there a way to load Caret¹s PALS-F99 deformation map onto wb_view?

Thanks
Saad



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

[Harwell, John]

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 
Overlay/Underlay - Surface page.


On Apr 12, 2018, at 7:41 AM, Saad Jbabdi 
<saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

Hi John

When I follow your steps it produces an empty func file:


http://www.nitrc.org/frs/download.php/1594/gifti.dtd;>
http://www.w3.org/2001/XMLSchema-instance;
  
xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd;
  Version="1.0"
  NumberOfDataArrays="0">
   
  
 
 
  
  
 
 
  
  
 
 
  
  
 
 
  
  
 
 
  
   
   




On 11 Apr 2018, at 19:24, Harwell, John 
<jharw...@wustl.edu<mailto:jharw...@wustl.edu>> wrote:

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 Encoding is XML.
* Click the Save button.

This should create a GIFTI functional file that can be loaded into wb_view.

John H

On Apr 11, 2018, at 12:47 PM, Saad Jbabdi 
<saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

Hi Matt

Thanks. But I am not sure I was clear enough so let me rephrase: is there a way 
to somehow export the attached map from Caret into a func.gi file that I can 
open in wb_view?

Thanks!
Saad



On 11 Apr 2018, at 16:36, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:

Hi Saad,

Not that I am aware of.  Probably better to generate distortion maps (e.g.
isotropic and anisotropic strains).

Matt.

On 4/11/18, 10:28 AM, 
"hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 on behalf of
Saad Jbabdi" 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 on behalf of
saad.jba...@ndcn.ox.ac.uk<mailto:saad.jba...@ndcn.ox.ac.uk>> wrote:

Hi all,

Is there a way to load Caret¹s PALS-F99 deformation map onto wb_view?

Thanks
Saad



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

[Harwell, John]

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 Encoding is XML.
* Click the Save button.

This should create a GIFTI functional file that can be loaded into wb_view.

John H

On Apr 11, 2018, at 12:47 PM, Saad Jbabdi 
> wrote:

Hi Matt

Thanks. But I am not sure I was clear enough so let me rephrase: is there a way 
to somehow export the attached map from Caret into a func.gi file that I can 
open in wb_view?

Thanks!
Saad



On 11 Apr 2018, at 16:36, Glasser, Matthew 
> wrote:

Hi Saad,

Not that I am aware of.  Probably better to generate distortion maps (e.g.
isotropic and anisotropic strains).

Matt.

On 4/11/18, 10:28 AM, 
"hcp-users-boun...@humanconnectome.org
 on behalf of
Saad Jbabdi" 

 on behalf of
saad.jba...@ndcn.ox.ac.uk> wrote:

Hi all,

Is there a way to load Caret¹s PALS-F99 deformation map onto wb_view?

Thanks
Saad



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

[Harwell, John]

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 google searches, this XCB error is reported with other applications.  
The neurodebian version of Workbench may still be using Qt 4 (The qt version is 
available in wb_view by selecting File Menu —> About Workbench and then 
clicking the More button).  Qt 5 provides better support for the XCB libraries.

John Harwell


On Mar 7, 2018, at 7:46 AM, Claude Bajada 
> wrote:


apologies Ubuntu 16.04 LTS installed from the neurodebian repo

On l-Erbgħa, 07 ta Mar, 2018 02:44 , Glasser, Matthew wrote:
What OS is this on?

Peace,

Matt.

From: 
>
 on behalf of Claude Bajada 
>
Date: Wednesday, March 7, 2018 at 4:25 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Problem creating scenes in wb_view


Hi all,

I am encountering a problem when trying to create a scene with wb_view. As soon 
as I try to add my scene I get a core dump:

Anyone has a similar problem and know a solution?

Claude




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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

[Harwell, John]

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 loading more images with setting created for illustration of 
> brain results and need to restart all over -even it requires to restart the 
> computer to have it working properly. I have installed last version in 
> Applications, and I am using a Mac Pro (Late 2013). What specs are needed to 
> diagnose this problem and solve it?
> 
> Thanks,
> 
> L
> 
> 
> 
> 
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Re: [HCP-Users] gif surface to obj

[Harwell, John]

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 
> wrote:

Hi all,

Does human connectome workbench have a tool to convert gii surfaces to obj?

Thanks,
Kamal

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

[Harwell, John]

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 is 
displayed describing border drawing.

* A mouse click adds a single border point.
* Hold down the Control  (Command Key on Mac) and Shift keys while dragging the 
mouse (hold left mouse button down while moving the mouse) to continuously add 
border points.
* Hold down Shift key and drag mouse to pan the surface.
* Hold down Control (Command on Mac) key and drag mouse to zoom the surface.
* Drag the mouse to rotate the surface.

John Harwell

On Feb 5, 2018, at 4:43 PM, Johanne Solis 
> wrote:

Hello ,
While trying to draw borders on workbench, I all of sudden couldn't drag the 
marker to make a border. I more so now plot points (red) around a section of my 
interest and it saves as a border. Did this change for anyone else? As much as 
I try to use the alt left click command , I can't drag to draw. Was this 
drawing feature changed in workbench ? And if not any idea what I could be 
doing wrong?

Thank you,
Johanne S.

--
johanne.so...@rutgers.edu
johanne.so...@gmail.com


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Re: [HCP-Users] Connectome Workbench Config File

[Harwell, John]

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) in 
the XDG_CONFIG_HOME directory and you may need to set permissions on the 
directory and/or config file.  It appeared to work for me on Linux but not on a 
Mac.

Otherwise, if you are on a Unix-type system, you could put a copy of a 
“Caret7.conf” file into a directory that is accessible by all users.  After 
that, replace each user’s Caret7.conf file with a symbolic link to the shared 
Caret7.conf file.

Be aware that the Caret7.conf file is used by both wb_command and wb_view.

John

On Jan 5, 2018, at 9:12 AM, Eric Earl > 
wrote:

Hi,

I don’t know if this might be just a question for Tim Coalson or if anyone else 
might know.

Connectome Workbench has a file for saving your configuration options here:

~/.config/brainvis.wustl.edu/Caret7.conf

Is there a way (or would it be easy to program a way) to allow for a 
non-default config file?  My problem comes out of trying to use:

wb_command -show-scene …

We want many users to all be ensured to have the same config file for the 
script using this command.  Thank you for any thoughts or help you can provide.

Warm Regards,
Eric Earl, Senior Research Assistant
Fair Neuroimaging Lab, Mackenzie Hall 2198
http://www.ohsu.edu/fair-lab

e...@ohsu.edu
Phone: 503-494-9732
Fax: 503-494-9988

Department of Behavioral Neuroscience
OHSU, Mail code: L470
3181 S.W. Sam Jackson Park Rd.
Portland, Oregon 97239


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

[Harwell, John]

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 macOS Sierra 
> version 10.12.5 on a Mac Pro (Late 2013). Could it be related to memory? My 
> Mac contains 4 memory slots, and all memory slots are currently in use.
> 
> Here I pasted the entire problem report for wb_view.:
> 
> Process:   wb_view [25125]
> Path:  
> /usr/local/workbench/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
> Identifier:workbench
> Version:   1.1.1 (1.1.1)
> Code Type: X86-64 (Native)
> Parent Process:??? [25123]
> Responsible:   wb_view [25125]
> User ID:   501
> 
> Date/Time: 2017-12-26 15:14:16.054 -0500
> OS Version:Mac OS X 10.12.5 (16F73)
> Report Version:12
> Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8
> 
> 
> Time Awake Since Boot: 95 seconds
> 
> System Integrity Protection: enabled
> 
> Crashed Thread:0  Dispatch queue: com.apple.main-thread
> 
> Exception Type:EXC_BAD_ACCESS (SIGSEGV)
> Exception Codes:   KERN_INVALID_ADDRESS at 0x
> Exception Note:EXC_CORPSE_NOTIFY
> 
> Termination Signal:Segmentation fault: 11
> Termination Reason:Namespace SIGNAL, Code 0xb
> Terminating Process:   exc handler [0]
> 
> VM Regions Near 0:
> --> 
>__TEXT 0001-000101965000 [ 25.4M] r-x/rwx 
> SM=COW  /usr/local/workbench/macosx64_apps/wb_view.app/Contents/MacOS/wb_view
> 
> Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
> 0   QtGui 0x000101f8c678 
> QMacInputContext::reset() + 872
> 1   com.apple.AppKit  0x7fff9f95d19f 
> -[NSTextInputContext(NSInputContext_WithCompletion) 
> selectedRangeWithCompletionHandler:] + 66
> 2   com.apple.AppKit  0x7fffa006f16f -[NSTextInputContext 
> tryHandleTSMEvent_offsetToPos_markedOrSelRange_withContext:markedOrSelRangeDispatchCondition:markedRangeContinuation:selectedRangeContinuation:continuation:]
>  + 181
> 3   com.apple.AppKit  0x7fffa0072b0f 
> __55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke.564 
> + 320
> 4   com.apple.AppKit  0x7fff9f836ec2 -[NSTextInputContext 
> handleTSMEvent:completionHandler:] + 1488
> 5   com.apple.AppKit  0x7fff9f836883 _NSTSMEventHandler + 
> 321
> 6   com.apple.HIToolbox   0x7fffa10dfd85 
> DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 
> 1708
> 7   com.apple.HIToolbox   0x7fffa10deff6 
> SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, 
> HandlerCallRec*) + 428
> 8   com.apple.HIToolbox   0x7fffa10dee3f 
> SendEventToEventTargetWithOptions + 43
> 9   com.apple.HIToolbox   0x7fffa11366d6 
> SendTSMEvent_WithCompletionHandler + 408
> 10  com.apple.HIToolbox   0x7fffa12ea61c 
> __SendTextInputEvent_WithCompletionHandler_block_invoke + 584
> 11  com.apple.HIToolbox   0x7fffa12e892d 
> SendTextInputEvent_WithCompletionHandler + 1154
> 12  com.apple.HIToolbox   0x7fffa135a5b5 -[IMKInputSession 
> _postEvent:completionHandler:] + 176
> 13  com.apple.HIToolbox   0x7fffa135a47f -[IMKInputSession 
> _createAndSendOffsetToPointEvent:completionHandler:] + 281
> 14  com.apple.HIToolbox   0x7fffa136f157 -[IMKInputSession 
> attributesForCharacterIndex_andLineRect:completionHandler:] + 591
> 15  com.apple.HIToolbox   0x7fffa136fde3 -[IMKInputSession 
> attributesForCharacterIndex:completionHandler:] + 80
> 16  com.apple.HIToolbox   0x7fffa135c2f5 
> __60-[IMKInputSession imkxpc_attributesForCharacterIndex:reply:]_block_invoke 
> + 505
> 17  com.apple.CoreFoundation  0x7fffa1bc722c 
> __CFRUNLOOP_IS_CALLING_OUT_TO_A_BLOCK__ + 12
> 18  com.apple.CoreFoundation  0x7fffa1ba83c4 __CFRunLoopDoBlocks 
> + 356
> 19  com.apple.CoreFoundation  0x7fffa1ba7b35 __CFRunLoopRun + 917
> 20  com.apple.CoreFoundation  0x7fffa1ba7544 CFRunLoopRunSpecific 
> + 420
> 21  com.apple.HIToolbox   0x7fffa134419e 
> -[IMKInputSessionXPCInvocation invocationAwaitXPCReply] + 606
> 22  com.apple.HIToolbox   0x7fffa1348a7c -[IMKInputSession 
> deactivate] + 2969
> 23  com.apple.HIToolbox   0x7fffa12fa7db 
> IMKInputSessionDeactivate + 36
> 24  com.apple.HIToolbox   0x7fffa12f9ba9 
> DeactivateInputMethodInstance + 100
> 25  com.apple.HIToolbox   0x7fffa12ee66d 
> 

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

[Harwell, John]

It is possible the file is corrupted.  Please try to run “wb_command 
-file-information  ” on the file and see if that works.

On Dec 12, 2017, at 12:20 PM, Marta Moreno 
<mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> wrote:

Thanks.

Yes, I can load spec files but when trying to see functional connectivity maps 
for the specific subject it crashes. I can load other type of files, i.e., seed 
used. This is the first time I cannot see this file, before I was able to do so 
without crashing. I have downloaded workbench v1.2.3. now but the problem 
persists. The only change I had these past weeks was the MATLAB_R2017b.


On Dec 12, 2017, at 1:12 PM, Harwell, John 
<jharw...@wustl.edu<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 use File Menu —> Open 
File and try opening just a surface file.


John Harwell


On Dec 12, 2017, at 11:25 AM, Marta Moreno 
<mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> wrote:

Dear experts,

I am getting an error any time I am trying to open file in wb_view. Any idea 
how to solve this problem?

Thanks,

-L

Error attached below:

Process:   wb_view [56364]
Path:  
/usr/local/workbench-new/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
Identifier:workbench
Version:   1.1.1 (1.1.1)
Code Type: X86-64 (Native)
Parent Process:??? [56362]
Responsible:   wb_view [56364]
User ID:   501

Date/Time: 2017-12-12 12:21:10.852 -0500
OS Version:Mac OS X 10.12.5 (16F73)
Report Version:12
Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8


Time Awake Since Boot: 270 seconds

System Integrity Protection: enabled

Crashed Thread:0  Dispatch queue: com.apple.main-thread

Exception Type:EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:   KERN_INVALID_ADDRESS at 0x
Exception Note:EXC_CORPSE_NOTIFY

Termination Signal:Segmentation fault: 11
Termination Reason:Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [0]


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

[Harwell, John]

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 11:25 AM, Marta Moreno  wrote:
> 
> Dear experts,
> 
> I am getting an error any time I am trying to open file in wb_view. Any idea 
> how to solve this problem? 
> 
> Thanks,
> 
> -L
> 
> Error attached below:
> 
> Process:   wb_view [56364]
> Path:  
> /usr/local/workbench-new/bin_macosx64/../macosx64_apps/wb_view.app/Contents/MacOS/wb_view
> Identifier:workbench
> Version:   1.1.1 (1.1.1)
> Code Type: X86-64 (Native)
> Parent Process:??? [56362]
> Responsible:   wb_view [56364]
> User ID:   501
> 
> Date/Time: 2017-12-12 12:21:10.852 -0500
> OS Version:Mac OS X 10.12.5 (16F73)
> Report Version:12
> Anonymous UUID:D5FF43E5-1CCA-5E9C-C5AF-22ACAE67AFE8
> 
> 
> Time Awake Since Boot: 270 seconds
> 
> System Integrity Protection: enabled
> 
> Crashed Thread:0  Dispatch queue: com.apple.main-thread
> 
> Exception Type:EXC_BAD_ACCESS (SIGSEGV)
> Exception Codes:   KERN_INVALID_ADDRESS at 0x
> Exception Note:EXC_CORPSE_NOTIFY
> 
> Termination Signal:Segmentation fault: 11
> Termination Reason:Namespace SIGNAL, Code 0xb
> Terminating Process:   exc handler [0]
> 
> 
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Re: [HCP-Users] RGBA files in connectome workbench

[Harwell, John]

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 a table 
of names.

John Harwell

On Dec 6, 2017, at 5:15 AM, Corina Melzer 
> wrote:

Hi,

I want to map some custom coloring to the triangles in wb_view and thought of 
using the RGBA files for that. I created this RGBA file with nibabel using 
values between [0,1].

gii_arr = gifti.GiftiDataArray(data=color_data,intent="NIFTI_INTENT_RGB_VECTOR")
gii_img = gifti.GiftiImage()
gii_img.add_gifti_data_array(gii_arr)
gifti.giftiio.write(gii_img, 'test.rgba.gii')

When loading this file into wb_view, all faces are coloured blue instead of the 
defined color codes.

How is this file supposed to be formatted to show the defined coloring? Am I 
getting the idea of this kind of file wrong?

I also tested with an rgb file which has been provided for caret some time ago 
(https://www.nitrc.org/forum/forum.php?offset=125_rows=25=flat_id=281_id=).
 The overlay is also just blue and not as shown in their provided screenshot.

[workbench version 1.2.3]

Thanks for your help,
Corina






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

[Harwell, John]

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 notes imply that 
"source $FREESURFER_HOME/sources.sh” may be needed in the Mac version of 
wb_shortcuts.

Related link: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/051087.html

John Harwell

On Nov 27, 2017, at 6:18 PM, Timothy Coalson 
> wrote:

The wb_shortcuts command is actually just a bash script.  However, it calls 
other utilities, and that function specifically calls both "mris_convert" and 
"wb_command".  Since it is complaining about "libgomp" which is involved in 
parallelization, it may in fact be an issue with wb_command, as I don't know 
that we have tested it on the newest OS X.  The "lazy symbol binding" suggests 
that you might have to run a command that actually uses parallelization to find 
out, however.  The easiest command to try this with may be "wb_command 
-signed-distance-to-surface" (run it with any surfaces, and see if it crashes 
similarly).

If it is in fact a problem with wb_command on the newest OS X, then you could 
compile it yourself from source while we figure out how to manage the OS 
version transition:

https://github.com/Washington-University/workbench/tree/v1.2.3

Tim


On Mon, Nov 27, 2017 at 6:01 PM, Kelly Martin 
> wrote:
Hi all,

I am using wb_shortcuts to map from native individual Freesurfer space to cifti 
format. I successfully ran Freesurfer's recon-all on my subjects. I downloaded 
the standard_mesh_atlases, and intended to map the individual lh.white and 
lh.pial (converted to .gii) to the 
fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii.

This is the command that I ran:

wb_shortcuts -freesurfer-resample-prep $SUBJECTS_DIR/SPCh061/surf/lh.white.gii 
$SUBJECTS_DIR/SPCh061/surf/lh.pial.gii 
$SUBJECTS_DIR/SPCh061/surf/lh.sphere.reg.gii 
/Users/newportlab/Applications/workbench/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii
 lh.midthickness.surf.gii SPCh061.lh.midthickness.32k_fs_LR.surf.gii 
lh.sphere.reg.surf.gii

And this was the resulting error:

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from: 
/Users/newportlab/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address

  Referenced from: 
/Users/newportlab/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib

/Users/newportlab/Applications/workbench/bin_macosx64/wb_shortcuts: line 285: 
22711 Abort trap: 6

I have tried installing and testing MacPorts, and running fs_update, with no 
success. Sierra has given Freesurfer users some grief, but since I have been 
able to run other Freesurfer commands successfully, I am wondering if it is 
something within the wb_shortcuts that is incompatible. Does anyone know of a 
work-around for this?

Thank you!

Kelly

--
Kelly Martin
Graduate Student
Interdisciplinary Program in Neuroscience
Georgetown University

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

[Harwell, John]

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 
> wrote:

Hi,

I'm writing a small python GUI application that generates CIFTI files. I want 
to add a button that opens several CIFTI files in the same wb_view window. I 
tried to use the command line "wb_view" and add the file names as parameters, 
but each time I call it, a new window of wb_view is opened. Does anyone know a 
better way to do it?

Best,
Keren

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Re: [HCP-Users] Neigbours about a vertex

[Harwell, John]

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 Workbench’s “wb_command 
-gifti-convert”.  There is also support for GIFTI in Matlab: 
http://www.artefact.tk/software/matlab/gifti/

The GIFTI Surface File contains two sections: (1) The XYZ coordinates for each 
vertex, and (2) Vertex indices that form the triangles (three consecutive 
vertex indices form one triangle).  There is no explicit neighbor information 
but it can be derived from triangle specifications.

John Harwell

On May 8, 2017, at 1:56 AM, 
luqi.cheng@gmail.com wrote:

Dear HCP Experts,

  I known that a surface(e.g. .white.surf.gii) is formed by a series of 
vertices. A triangle is formed by three vertices and three sides. But I have no 
idea how to get the neigbours, like vertices and sides,  of a vertex from a 
surface file. And how the three vertices form the triangles?

Thanks,
Luqi

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

[Harwell, John]

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 should be consistent.

We use QSettings (look for Platform-Specifici Notes in 
http://doc.qt.io/qt-5/qsettings.html) for the wb_view/wb_command preferences 
and the location and format of the preferences are system dependent.  The 
location and name of the preferences file will vary, depending upon the system. 
 On Mac, the name is ~/Library/Preferences/edu.wustl.brainvis.Caret7.plist.  On 
our Ubuntu Linux, I found the preferences in 
~/.config/brainvis.wustl.edu/Caret7.conf.

John Harwell

On May 2, 2017, at 8:58 AM, Keith Jamison 
> wrote:

I'm trying to save some images using wb_command -show-scene, and I can't figure 
out how to change settings for things like cross-hairs or slice labels.  I know 
I can change these in the wb_view Preferences window in the Volume tab, but I'm 
hoping to script the whole process and get consistent results.  So...

1. Is there a parameter in the .scene file to control these kind of display 
settings?
2. Where are the wb_view preferences stored?  Though not ideal, I guess my 
script could modify the preferences file before running wb_command -show-scene

Thanks!
Keith

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

[Harwell, John]

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 also appear that your computer is using the “Mesa” OpenGL libraries 
(/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1 is in the output you provided).  You 
should consider installing the OpenGL libraries provided by the manufacturer of 
your computer’s graphics card or updating the Mesa3D package on your computer.

John

On Mar 31, 2017, at 8:44 AM, Dev vasu 
>
 wrote:

Dear all ,

I am incurring some problems  when  i try to capture the image in Connectome 
workbench viewer , it seems some binaries are not working properly . the sample 
image output is attached for your reference ( .png file)  . The error that i am 
getting is listed below


" WARNING: X Error: GLXBadContext 172
  Extension:155 (Uknown extension)
  Minor opcode: 6 (Unknown request)
  Resource id:  0x3e000b7
wb_view(_ZN5caret15SystemUtilities12getBackTraceERSt6vectorINS_7AStringESaIS2_EE+0x72)
 [0xf81eb2]
wb_view(_ZN5caret15SystemUtilities12getBackTraceEv+0x4e) [0xf81ffe]
wb_view() [0x6ce28b]
/usr/lib/x86_64-linux-gnu/libQtCore.so.4(_Z17qt_message_output9QtMsgTypePKc+0x2f)
 [0x7feb6db1ce9f]
/usr/lib/x86_64-linux-gnu/libQtCore.so.4(+0x70371) [0x7feb6db1d371]
/usr/lib/x86_64-linux-gnu/libQtCore.so.4(_Z8qWarningPKcz+0xa1) [0x7feb6db1d5e1]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(+0x2330e6) [0x7feb6e76e0e6]
/usr/lib/x86_64-linux-gnu/libX11.so.6(_XError+0x11d) [0x7feb6bb71c4d]
/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1(+0x1d402) [0x7feb6d3cd402]
/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1(+0x1af82) [0x7feb6d3caf82]
/usr/lib/x86_64-linux-gnu/libQtOpenGL.so.4(_ZN10QGLContext13chooseContextEPKS_+0x5b8)
 [0x7feb6f2dad88]
/usr/lib/x86_64-linux-gnu/libQtOpenGL.so.4(_ZN10QGLContext6createEPKS_+0x3d) 
[0x7feb6f25dc6d]
/usr/lib/x86_64-linux-gnu/libQtOpenGL.so.4(_ZN9QGLWidget12renderPixmapEiib+0x1b1)
 [0x7feb6f265511]
wb_view(_ZN5caret17BrainOpenGLWidget12captureImageEPNS_17EventImageCaptureE+0x2cf)
 [0x70b9cf]
wb_view(_ZN5caret17BrainOpenGLWidget12receiveEventEPNS_5EventE+0x212) [0x70bd62]
wb_view(_ZN5caret12EventManager9sendEventEPNS_5EventE+0x69d) [0xf4c06d]
wb_view(_ZN5caret18ImageCaptureDialog18applyButtonClickedEv+0x14d) [0x7398bd]
/usr/lib/x86_64-linux-gnu/libQtCore.so.4(_ZN11QMetaObject8activateEP7QObjectPKS_iPPv+0x4d0)
 [0x7feb6dc4c010]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(_ZN16QDialogButtonBox7clickedEP15QAbstractButton+0x3f)
 [0x7feb6eb0735f]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(+0x5cc414) [0x7feb6eb07414]
/usr/lib/x86_64-linux-gnu/libQtCore.so.4(_ZN11QMetaObject8activateEP7QObjectPKS_iPPv+0x4d0)
 [0x7feb6dc4c010]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(_ZN15QAbstractButton7clickedEb+0x42) 
[0x7feb6eda4d12]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(+0x59f2b3) [0x7feb6eada2b3]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(+0x5a0664) [0x7feb6eadb664]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(_ZN15QAbstractButton17mouseReleaseEventEP11QMouseEvent+0x74)
 [0x7feb6eadb774]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(_ZN7QWidget5eventEP6QEvent+0x2a0) 
[0x7feb6e7568d0]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(_ZN19QApplicationPrivate13notify_helperEP7QObjectP6QEvent+0x8c)
 [0x7feb6e6fffdc]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(_ZN12QApplication6notifyEP7QObjectP6QEvent+0x476)
 [0x7feb6e7070d6]
/usr/lib/x86_64-linux-gnu/libQtCore.so.4(_ZN16QCoreApplication14notifyInternalEP7QObjectP6QEvent+0x8d)
 [0x7feb6dc3790d]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(_ZN19QApplicationPrivate14sendMouseEventEP7QWidgetP11QMouseEventS1_S1_PS1_R8QPointerIS0_Eb+0x14d)
 [0x7feb6e7066dd]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(+0x2493f2) [0x7feb6e7843f2]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(_ZN12QApplication15x11ProcessEventEP7_XEvent+0x16b3)
 [0x7feb6e783c83]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(+0x272542) [0x7feb6e7ad542]
/lib/x86_64-linux-gnu/libglib-2.0.so.0(g_main_context_dispatch+0x2a7) 
[0x7feb6b1f2197]
/lib/x86_64-linux-gnu/libglib-2.0.so.0(+0x4a3f0) [0x7feb6b1f23f0]
/lib/x86_64-linux-gnu/libglib-2.0.so.0(g_main_context_iteration+0x2c) 
[0x7feb6b1f249c]
/usr/lib/x86_64-linux-gnu/libQtCore.so.4(_ZN20QEventDispatcherGlib13processEventsE6QFlagsIN10QEventLoop17ProcessEventsFlagEE+0x9e)
 [0x7feb6dc682ce]
/usr/lib/x86_64-linux-gnu/libQtGui.so.4(+0x272616) [0x7feb6e7ad616]
/usr/lib/x86_64-linux-gnu/libQtCore.so.4(_ZN10QEventLoop13processEventsE6QFlagsINS_17ProcessEventsFlagEE+0x3f)
 [0x7feb6dc3618f]
/usr/lib/x86_64-linux-gnu/libQtCore.so.4(_ZN10QEventLoop4execE6QFlagsINS_17ProcessEventsFlagEE+0x1b5)
 [0x7feb6dc364f5]
/usr/lib/x86_64-linux-gnu/libQtCore.so.4(_ZN16QCoreApplication4execEv+0x99) 
[0x7feb6dc3c4b9]
wb_view(main+0x16a5) [0x6b29c5]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) 

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

[Harwell, John]

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 (number 
with up and down arrows) of the row containing your GIFTI file.  Press the up 
arrow on your keyboard to move to the next map and continue pressing the up 
arrow to sequence through all of the maps (You can also click the small up 
arrow next to the map index).
* Press the Record button on the Animation Control Dialog and a dialog will 
appear asking for the name of your movie file.  Enter a name for the file (I 
think the name should end in “.mpg”) and press the Save button to create the 
movie file.

As far as I know, there is no way to automatically sequence through all maps in 
a data file.

John Harwell

On Feb 26, 2017, at 1:52 AM, Kristian M. Eschenburg 
> wrote:

Hi all

I have a large matrix of size NxT, with N observations and T time points.  I'm 
able to convert this matrix into a gifti .func file using Matlab, load this 
single file into the Workbench, and view each time point T as a single map.  
However, I want to convert it to a "time series" file and then animate it in 
the Connectome Workbench viewer.  How can I go about doing this?

I've looked at the "Animation Control" window, but when I try to record 
something, no files are created.

Could you shed light on this?

Thanks!


Kristian

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

[Harwell, John]

Your file appears to be a NIFTI volume file.  Use the command “wb_command 
-volume-label-import”.  This command adds labels to the volume file’s header 
and creates a new NIFTI volume that is viewable in wb_view.

On Feb 13, 2017, at 1:43 PM, Xavier Guell Paradis 
<xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote:

Dear John,
My file is a cerebellum map: 
Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii. This file 
contains integers from 1 to 7 for the cerebellar structures.
I have tried -cifti-label-import and -metric-label-import but they do not seem 
to work. Which wb command would 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 [jharw...@wustl.edu<mailto:jharw...@wustl.edu>]
Sent: Monday, February 13, 2017 1:07 PM
To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: [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 to the integer values 
in the label table.

Without knowing the format of your data, I am unable to suggest the best 
“wb_command” for you to use but one of these may be useful:
* wb_command -cifti-create-label
* wb_command -cifti-label-import
* wb_command -metric-label-import

Related questions have been asked previously and these are links to them from 
the HCP user archives:
* http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02286.html
* http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01919.html
* http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02548.html

John Harwell



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 Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>>
Sent: Monday, February 13, 2017 11:05 AM
To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: [HCP-Users] Edit colors of palette in wb view?

Dear HCP experts,
Is it possible to edit the colors of the palette in wb view? For example, is it 
possible to define color A, color B and color C and tell wb view to show 
values=1 in color A, values=2 in color B, values=3 in color C, etc.?
Thank you very much,
Xavier.
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[HCP-Users] Edit colors of palette in wb view?

[Harwell, John]

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 to the integer values 
in the label table.

Without knowing the format of your data, I am unable to suggest the best 
“wb_command” for you to use but one of these may be useful:
* wb_command -cifti-create-label
* wb_command -cifti-label-import
* wb_command -metric-label-import

Related questions have been asked previously and these are links to them from 
the HCP user archives:
* http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02286.html
* http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01919.html
* http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02548.html

John Harwell



From: 
hcp-users-boun...@humanconnectome.org
 
>
 on behalf of Xavier Guell Paradis >
Sent: Monday, February 13, 2017 11:05 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Edit colors of palette in wb view?

Dear HCP experts,
Is it possible to edit the colors of the palette in wb view? For example, is it 
possible to define color A, color B and color C and tell wb view to show 
values=1 in color A, values=2 in color B, values=3 in color C, etc.?
Thank you very much,
Xavier.
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[HCP-Users] Solution for: Continuous border drawing holding "alt/option" key does not work

[Harwell, John]

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 something wrong in my computer?

Solution: Continuous border drawing was changed to holding both SHIFT and CTRL 
(Command key on Mac) keys. Information is displayed in the Border toolbar’s 
“New” button tooltip (hover over the New button with your mouse to see the 
tooltip).

John Harwell


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