Re: [HCP-Users] Unable to Capture image using Wb_view

One of the methods to capture images (render pixmap) is not supported well by intel GPUs. We use nvidia GPUs in the linux computers we run workbench on, and they generally work well for us. One workaround is to switch the image capture method in wb_view -> Preferences -> OpenGL to "Grab Frame

[HCP-Users] Unable to Capture image using Wb_view

Dear Sir, I am facing problems in capturing an imaging using wb_view , Currently i am running on Ubuntu 16.04 Xenial I am annexing the error that i am getting in txt file and the image (label.png), please kindly review the attachment and let me know if there is any fault with in my system.

Re: [HCP-Users] Surfaces, coordinates and beginner questions

This is not something that QC can catch, it requires extensive processing to discover this. The individual subject parcellations that are generated during the MMP 1.0 process do reflect these differences, so these will be able to be used instead of the group label map when using HCP data. I

Re: [HCP-Users] Fw: rfMRI data files

Hi Heracles, FAQ #3 on the HCP-Users FAQ might help you do what Matt is suggesting. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of

Re: [HCP-Users] ERROR: Unexpected parameter: -local-affine-method

That is a new option that is not yet in a released version of workbench, and was probably not intended to be pushed to the pipelines repository. You can use github to find the version before that line was added, and use that instead. Alternatively, you can probably just comment out that line and

Re: [HCP-Users] rfMRI data files

Hi Romuald, The phase encoding direction will affect areas of signal dropout in the images. This is discussed in the Smith et al. 2013 paper on Resting State fMRI in HCP, so you might start there. Best, Jenn Jennifer Elam, Ph.D. Scientific

Re: [HCP-Users] How to transform all subcortical values to 0 in a dscalar?

You can use -cifti-replace-structure with the -volume-all option and a volume file of zeroes. If you have a lot of maps (or you want to do something similar to a long dtseries), you can make a cifti file with 1's in the surfaces and 0's in voxels, and use -cifti-math to multiply them together.

Re: [HCP-Users] rfMRI data files

Hi, Just to follow up on your answer and understand better - does the encoding direction introduce some bias (i.e. I mean some non neural component) into the signal? If it is necessary to analyze an equal amount of each direction that means that some effect cancels out? Is it known what it is? Is

Re: [HCP-Users] Surfaces, coordinates and beginner questions

Thanks for the detailed explanations! I have just one follow up question regarding this point: On Tue, Oct 3, 2017 at 11:57 PM, Timothy Coalson wrote: > > > Some techniques like hyperalignment use this "correspondence" concept > aggressively, and allow you to have

[HCP-Users] Fw: rfMRI data files

Does anyone know how the concatenation (see discussion below) of the ROI extracted time series needs to happen? Do I simply concatenate the time series as a temporal sequence, rfMRI_REST2_LR followed by rfMRI_REST2_RL ? Thanks again for the kind help. Heracles Panagiotides, PhD From:

[HCP-Users] ERROR: Unexpected parameter: -local-affine-method

Dear HCP experts, I am trying to run the HCP Pipeline scripts on the tutorial data (100307). When I run the script PostFreeSurferPipelineBatch.sh, I get following error after the wb_command: While running: /opt/ni_tools/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command

Re: [HCP-Users] NEO-FFI Agreeableness scoring

Hi Josh, After a couple of spot checks, it appears that you might have indeed found a bug in the NEO Agreeableness scoring. Thanks for posting the problem to the list. We will pass the issue on to the developers and see if they can find the bug and correct their code for the scoring. The

[HCP-Users] How to transform all subcortical values to 0 in a dscalar?

Dear HCP experts, I have a dscalar file with one map of cortical and subcortical data. I would like to transform all subcortical values to 0, and leave the cortical surface values intact. I have explored the -cifti-stats and -volume-stats options as well as -cifti-create-dense-scalar but cannot

[HCP-Users] NEO-FFI Agreeableness scoring

Hello, I believe that I may have found a bug in the total score of Agreeableness as it is presented in the HCP data. It appears that when I run syntax on the raw data (coding SD = 0, D = 1, N = 2, A = 3, SA = 4) and then reverse code appropriate items and sum into subscales, all of the subscales