[HCP-Users] Workbench v1.3.2 Released

[Elam, Jennifer]

News from the Human Connectome Project (HCP)
August 28, 2018

Connectome Workbench v1.3.2 Released
Announcing the release of version 1.3.2 of Connectome 
Workbench 
(WB) brain visualization and analysis software. This release fixes a few bugs 
and adds some features, most notably Annotation substitutions, which allows one 
to efficiently make a series of annotations (text labels) with content loaded 
from a CSV file (*.wb_annsub.csv).

The Workbench distribution, available for 64-bit Mac OSX, Windows, and Linux, 
includes wb_view, a GUI-based visualization platform, and wb_command, a 
command-line program for performing a variety of algorithmic tasks using 
volume, surface, and grayordinate data.

Changes in Workbench v1.3.2
wb_view:
New Features

  *   Yoked annotation substitutions (and updates in Workbench Help and Guide 
to 
Annotations)
  *   Updates to BALSA Upload dialog including notification of updated 
extraction directory prefix
  *   Tab number always included in the name of the tab since some GUI controls 
(volume surface outline) use the tab number

Bug Fixes

  *   Fixes for sizing of color bars
  *   Missing QT SVG library has been added to Linux distributions

wb_command:
New Features

  *   new -surface-geodesic-all-to-all command
  *   fwhm estimation now has "whole file" and "demean" options

Notes on launching Workbench: (1) wb_command must be run from a terminal window 
(not double-clicked on Mac or Windows); (2) wb_view may crash if used with a 
remote desktop due to problems with Xcb and OpenGL in the remote desktops.  
VirtualGL works for some users.  Even if wb_view runs in a remote desktop, 
performance may be poor as they often use software implementations of OpenGL.

WB v1.3.2 is compatible with the WB v1.0 tutorial and the processed 1200 
Subjects Group Average Data available to download at 
http://humanconnectome.org/connectome/get-connectome-workbench.html and on the 
ConnectomeDB HCP project 
page. Access to both 
datasets require ConnectomeDB login and signature of the HCP Open Access Data 
Use Terms.

To download the WB v1.3.2 source code from 
GitHub: follow the link, 
click Releases (near the top center of the page), then under v1.3.2, click the 
“Source code (zip)” or “Source code (tar.gz)” button.
Discussion of Connectome Workbench usage, bugs, and features can be posted to 
the hcp-users discussion list (sign up 
here).

Best,
The WU-Minn HCP Consortium


Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org


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Re: [HCP-Users] two maximum points using -metric-extrema

[Xinyang Liu]

Dear experts,


Could I ask an additional question following my previous emails about the CIFTI 
data display? 


If two surface ROIs of one .func.gii  file are displayed in separate maps of 
Connectome Workbench instead of simultaneously shown on one brain surface, does 
it mean the two ROIs are saved separately with two sets of global grayordinate 
coordinates? Thanks.


Best regards,
Xinyang



At 2018-08-27 11:16:42, "Glasser, Matthew"  wrote:

Would have to ask that on the FSL list.


Matt.


From: Xinyang Liu 
Date: Sunday, August 26, 2018 at 10:14 PM
To: Matt Glasser 
Cc: Timothy Coalson , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Hi, Matt.
I saw the second ROI on WB as you said then. Thank you so much！


Then another left question is, when I use $FSL/surf2surf to change the 
.func.gii file (with two ROIs included) to .asc format, I only saw the  
coordinates information of one ROI (vertices with 1 values). The .func.gii 
showed vertex number of two ROIs, i.e. 127, 48. But when checking the 
transformed .asc file, I only found the ROI coordinates of the first ROI (127 
vertices), not the second. 


Does it mean the two produced ROIs are saved separately in .func.gii, but the 
"surf2surf "command can only transform one of them to .asc?



Best regards,
Xinyang



At 2018-08-27 01:12:54, "Glasser, Matthew"  wrote:

The other should be in the next map of the ROI file.


Matt.


From: Xinyang Liu 
Date: Sunday, August 26, 2018 at 2:41 AM
To: Matt Glasser 
Cc: Timothy Coalson , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Hi, Matt.
Sure. I attached two pictures and two produced GIFTI files here. 


In data processing, I first used -metric-extrema to find the maximum point 
within a certain fMRI region. The "maximum_IPS.JPG" attached was among the 
condition that two maximum points were found (please see the two yellow points 
in the first attached picture). The corresponding GIFTI file is 
"L.maxima.func.gii".


Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to 
draw ROIs, the result only showed one created ROI based on one maximum point, 
as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" 
file is also attached.


I also used the -metric-stats to calculate the vertex number of the created 
ROI, but the result provided two values: 127, 48.


So I am quite confusing about what happened here.


Best regards,
Xinyang





At 2018-08-26 13:03:42, "Glasser, Matthew"  wrote:

How about posting some screen captures so we know what is happening?


Matt.


From: Xinyang Liu 
Date: Saturday, August 25, 2018 at 11:51 PM
To: Timothy Coalson 
Cc: Matt Glasser , HCP 讨论组 
Subject: Re: [HCP-Users] two maximum points using -metric-extrema



Dear Tim, dear Matt,


Thank you very much for your helpful answers.


Sorry that I may not described very clearly before. As Tim mentioned, we used 
the -metric-extrema to find the maximum point within a certain region (produce 
"maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs 
(produced "ROI.func.gii" file). 


Then there is a contradictory thing emerged. When we used "wb_command 
-metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few 
results showed  two values, which might indicate two ROIs based on the two 
maximum points. We checked the maxima.func.gii files, and found there do 
existed two maximum points in such condition. However, when we looked at the 
created ROI images on Connectome Workbench, we only saw one target ROI drawn on 
the brain surface. This confused us a lot. We don't know whether there were one 
or two ROIs produced. Do you have any suggestions about that? Thanks.


Best regards,
Xinyang





At 2018-08-25 04:16:48, "Timothy Coalson"  wrote:

The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or 
-1 based on if they are a local maximum or minimum.  By default, if there are 
two equal values that are closer than the search range, then *neither* of them 
will be identified as an extrema.  If they are further then the search range, 
then both may be extrema.


The -consolidate-mode acts somewhat differently - if two equal values are 
touching, neither is treated as an initial extrema, but as long as there is at 
least one vertex separating them, they may both be treated as initial extrema.  
After the initial extrema are found, all extrema that are close to other 
extrema are "consolidated" together.  The details are somewhat complicated, and 
it was implemented by request of others, it is not something that we use.


Tim




On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu  wrote:

Hi, Matt. Thank you very much for your reply.


The extreme point was searched in a certain surface area. Do you mean that even 
there are two maximum points with the same value, they were controlled in a 
limited distance and therefore, the final drawn ROI is a combined region of two 

Re: [HCP-Users] two maximum points using -metric-extrema

[Timothy Coalson]

.func.gii files are simply arrays of values, where one dimension is the
number of vertices in the surface, and the other is the number of maps in
the file.  Every vertex of the relevant surface gets a value.  The special
case of "ROIs" is just that the values are all either 0 or 1.  So, while in
the second ROI map, different vertices have values of 1 than the first ROI
map, both maps span all vertices.

Surface coordinates are stored in .surf.gii files - neither .func.gii nor
cifti files contain vertex coordinates.  Cifti does not support using a
different set of brainordinates in different maps of the file - every map
in a single cifti file uses the same set of brainordinates.  Internally
cifti files are just another rectangular matrix, but used in a different
way (and with different, more elaborate metadata).

Tim


On Tue, Aug 28, 2018 at 10:55 PM, Xinyang Liu  wrote:

> Dear experts,
>
> Could I ask an additional question following my previous emails about the
> CIFTI data display?
>
> If two surface ROIs of one *.func.gii*  file are displayed in separate
> maps of Connectome Workbench instead of simultaneously shown on one brain
> surface, does it mean the two ROIs are saved separately with two sets of
> global grayordinate coordinates? Thanks.
>
> Best regards,
> Xinyang
>
>
> At 2018-08-27 11:16:42, "Glasser, Matthew"  wrote:
>
> Would have to ask that on the FSL list.
>
> Matt.
>
> From: Xinyang Liu 
> Date: Sunday, August 26, 2018 at 10:14 PM
> To: Matt Glasser 
> Cc: Timothy Coalson , HCP 讨论组 <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] two maximum points using -metric-extrema
>
> Hi, Matt.
> I saw the second ROI on WB as you said then. Thank you so much！
>
> Then another left question is, when I use $FSL/*surf2surf* to change the *
> .func.gii *file (with two ROIs included) to *.asc* format, I only saw the
> coordinates information of one ROI (vertices with 1 values). The
> .func.gii showed vertex number of two ROIs, i.e. 127, 48. But when checking
> the transformed .asc file, I only found the ROI coordinates of the first
> ROI (127 vertices), not the second.
>
> Does it mean the two produced ROIs are saved separately in .func.gii, but
> the "surf2surf "command can only transform one of them to .asc?
>
> Best regards,
> Xinyang
>
>
> At 2018-08-27 01:12:54, "Glasser, Matthew"  wrote:
>
> The other should be in the next map of the ROI file.
>
> Matt.
>
> From: Xinyang Liu 
> Date: Sunday, August 26, 2018 at 2:41 AM
> To: Matt Glasser 
> Cc: Timothy Coalson , HCP 讨论组 <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] two maximum points using -metric-extrema
>
> Hi, Matt.
> Sure. I attached two pictures and two produced GIFTI files here.
>
> In data processing, I first used *-metric-extrema* to find the maximum
> point within a certain fMRI region. The "maximum_IPS.JPG" attached was
> among the condition that two maximum points were found (please see the two
> yellow points in the first attached picture). The corresponding GIFTI file
> is "L.maxima.func.gii".
>
> Then I continued using the "L.maxima.func.gii" and
> *-metric-rois-from-extrema* to draw ROIs, the result only showed one
> created ROI based on one maximum point, as the second picture (IPS_ROI.JPG)
> attached. The "TARGET_ROI_IPS_L.func.gii" file is also attached.
>
> I also used the *-metric-stats* to calculate the vertex number of the
> created ROI, but the result provided two values: 127, 48.
>
> So I am quite confusing about what happened here.
>
> Best regards,
> Xinyang
>
>
>
> At 2018-08-26 13:03:42, "Glasser, Matthew"  wrote:
>
> How about posting some screen captures so we know what is happening?
>
> Matt.
>
> From: Xinyang Liu 
> Date: Saturday, August 25, 2018 at 11:51 PM
> To: Timothy Coalson 
> Cc: Matt Glasser , HCP 讨论组 <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] two maximum points using -metric-extrema
>
> Dear Tim, dear Matt,
>
> Thank you very much for your helpful answers.
>
> Sorry that I may not described very clearly before. As Tim mentioned, we
> used the -metric-extrema to find the maximum point within a certain region
> (produce "maxima.func.gii" file) and then use the -metric-rois-from-extrema
> to draw ROIs (produced "ROI.func.gii" file).
>
> Then there is a contradictory thing emerged. When we used "wb_command
> -metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a
> few results showed  two values, which might indicate two ROIs based on the
> two maximum points. We checked the maxima.func.gii files, and found there
> do existed two maximum points in such condition. However, when we looked
> at the created ROI images on Connectome Workbench, we only saw one target
> ROI drawn on the brain surface. This confused us a lot. We don't know
> whether there were one or two ROIs produced. Do you have any suggestions
> about that? Thanks.
>
> Best regards,
> Xinyang
>
>
>
> At 2018-08-25 04:16:48, "Timothy Coalson"  wrote:
>
> The -metric-extrema command