[HCP-Users] Pain intensity scores

Dear HCP team, I’m interested in the NIH Toolbox Pain Intensity measure (PainIntens_RawScore). However, the 500 Subject Release data dictionary states that it was “Excluded currently due to glitch in the Toolbox data download”, and it doesn’t seem to be mentioned in the updated 1200 Subject

Re: [HCP-Users] Workbench: save images using the command line

Hi Garren, One additional point in case it wasn’t yet clear. A scene file can contain many individual scenes. You have the option of creating a separate scene for each map (whether it’s a separate cifti file or one many-map cifti file) and then using show-scene to display successive scenes

Re: [HCP-Users] Workbench: save images using the command line

Awesome! Thank you all for the help. And for getting back to me so quickly! Cheers, -Garren On Mon, Jan 29, 2018 at 5:37 PM, Glasser, Matthew wrote: > Yes that is what I am suggesting you do. If you want to iterate over > files, you would have to use sed and find and

Re: [HCP-Users] Workbench: save images using the command line

Yes that is what I am suggesting you do. If you want to iterate over files, you would have to use sed and find and replace in the scene file. Peace, Matt. From: Garren Gaut > Date: Monday, January 29, 2018 at 5:36 PM To: "Elam, Jennifer"

Re: [HCP-Users] Workbench: save images using the command line

No, scene files are highly GUI-centric, taking captures of what is in a scene is somewhat secondary. The number of display options for files (and when we add new display features) would make it very cumbersome to make and maintain a command to do the equivalent without the GUI. You can set up a

Re: [HCP-Users] Workbench: save images using the command line

Hey All, I think I figured out why the save scene process is inefficient for me. My cifti files have 1 map per file, which would mean saving a scene file for each cifti file. It seems like the way workbench was designed (which i missed) is to put multiple maps in one file, save only one scene,

Re: [HCP-Users] Workbench: save images using the command line

I don't believe there is currently a way to create a scene file outside of the workbench GUI because several pieces of data that are saved in scene files (e.g. what files are loaded, layer settings, structure orientation, zoom level, panning, etc.) are set within the GUI. CC'ing Tim and John in

Re: [HCP-Users] Workbench: save images using the command line

Perhaps Jenn has some text about scenes you can read. The scene saves the exact state of workbench. You can then export pictures using the command I mentioned below. The development version allows you to iterate through multiple maps. Peace, Matt. From: Garren Gaut

Re: [HCP-Users] Workbench: save images using the command line

You have save a scene in workbench after you set everything up how you want it. Peace, Matt. From: Garren Gaut > Date: Monday, January 29, 2018 at 5:11 PM To: Matt Glasser > Subject: Re: [HCP-Users]

Re: [HCP-Users] Workbench: save images using the command line

wb_command -show-scene is used for this purpose. The development version allows you to increment by map index. Peace, Matt. From: > on behalf of Garren Gaut >

[HCP-Users] Workbench: save images using the command line

Hi HCP support, I am trying to automate the generation of brain images using workbench. I have several cifti files containing effect size maps and I would like to save the maps to images without ever using the workbench GUI. I've written a script that loads of all my files and sets up the viewing

Re: [HCP-Users] [SPAM] about the unrestricted data

Acquisition Q1- Q13 is the quarter the subject's data were collected in the HCP (collected 2012-2015). This is important because 1) some of the earlier data was reconstructed with a different reconstruction algorithm than data collected later, and 2) data has been released over the course of

Re: [HCP-Users] An error in Post-FreeSurfer Pipeline

gedit with bash shell highlighting (sh). Matt On 1/29/18, 11:50 AM, "Darko Komnenić" wrote: >Hi Matt, >could you please tell me which editor with shell syntax highlighting >you are using? I don't see any option to change the view/display mode >of the text in the one I have

Re: [HCP-Users] Convert dlabel to dscalar

Inline comments. Tim On Mon, Jan 29, 2018 at 9:51 AM, Xavier Guell Paradis wrote: > Dear HCP experts, > I have a dlabel file that labels a particular nucleus of the left thalamus > (thalamusnucleus.dlabel.nii). I would like to convert this dlabel file to a > whole-brain

Re: [HCP-Users] NIH-Toolbox

Hi Christopher, Higher scores should indicate better performance on the NIH Toolbox cognition tests. The scores should have a mean of 100 and standard deviation of 15 as normed against the nationally representative NIH Toolbox normative sample. More details on the scoring are available in the

Re: [HCP-Users] An error in Post-FreeSurfer Pipeline

Hi Matt, could you please tell me which editor with shell syntax highlighting you are using? I don't see any option to change the view/display mode of the text in the one I have installed on my computer. Thanks, Darko On 1/26/18, Glasser, Matthew wrote: > Here is the relevant

[HCP-Users] NIH-Toolbox

Dear HCP Team, Am I right with the presumption that for all NIH toolbox measures of cognitive function higher scores indicate better performance? I'm getting somewhat paradoxical results when looking at some of the cognitive measures (i.e. Flanker and DCST) so I just want to double-check...

[HCP-Users] Convert dlabel to dscalar

Dear HCP experts, I have a dlabel file that labels a particular nucleus of the left thalamus (thalamusnucleus.dlabel.nii). I would like to convert this dlabel file to a whole-brain dscalar file, so that this nucleus in the left thalamus has a value of 1 and the rest of the brain has a value of