Re: [HCP-Users] Palm with TFCE on Cifti data

Hi, I noticed the examples page has been updated. I wanted to ask why you switched from using wb_command -cifti-create-dense-scalar to wb_command -cifti-create-dense-from-template? Also, I think example 9 the naming of the files is off, probably copy and pasted from example 10. Given the

Re: [HCP-Users] ROIs and Betas from Cifti Data

I should probably rephrase some of -cifti-label-import help. When it says: "The label list file must have lines of the following format: " It means 2 lines per label: the first line is the label name, the second line is the numeric stuff, where is an integer that you will

Re: [HCP-Users] ROIs and Betas from Cifti Data

Thank you, I was using a bad input file. The command works now. for -cifti-label-import however, I am no sure how the label file is supposed to look. I get a malformed error: ERROR: label list file is malformed for entry #1: test 255 255 255 255 I have 4 cortical and 1 subcortical ROIs which

Re: [HCP-Users] ROIs and Betas from Cifti Data

What does the input data look like? Peace, Matt. From: "Michael F.W. Dreyfuss" > Date: Tuesday, September 20, 2016 at 1:22 PM To: Matt Glasser > Cc: "Michael F.W. Dreyfuss"

Re: [HCP-Users] ROIs and Betas from Cifti Data

When I run wb_command -cifti-find-clusters FoodNogo_results_merged_tfce_tstat_fwep.dscalar.nii 1 1 1 1 COLUMN FoodNogo_results_merged_tfce_tstat_fwep_ROIs.dscalar.nii I get the error: ERROR: left surface required but not provided Then if I add the option: -left-surface

Re: [HCP-Users] Lifespan Pilot Subject Scans

Hi David, You are right that there we did collect more data for the Lifespan Pilot Project that has not yet been released. The data were processed for use in the preliminary report, but we have since made some improvements to our processing pipelines and we have it on our to do list to

Re: [HCP-Users] ROIs and Betas from Cifti Data

If you are getting error messages, I recommend posting them. Peace, Matt. From: "Michael F.W. Dreyfuss" > Date: Tuesday, September 20, 2016 at 10:40 AM To: Matt Glasser >, Timothy Coalson

Re: [HCP-Users] Possible Typo in task fmri script

I agree that looks like a bug. The reason this is here is incase one has an ${fMRIName} that can be analyzed two different ways using different designs ${fsfName}. Peace, Matt. From: > on behalf of Andrew

Re: [HCP-Users] ROIs and Betas from Cifti Data

That makes sense if Z stats are not involved. Matt. From: "Harms, Michael" > Date: Tuesday, September 20, 2016 at 11:00 AM To: Matt Glasser >, "Michael F.W. Dreyfuss"

Re: [HCP-Users] Brain Atlas

The data are available here: https://balsa.wustl.edu/study/show/RVVG Peace, Matt. From: > on behalf of Leslie Huszar > Date: Tuesday, September

[HCP-Users] Brain Atlas

To Whom it May Concern: Dr. Huszar is wanting to find out how to view the Brain Atlas developed by Dr. Matthew Glasser and Dr. David Van Essen. He read the article in the* Neurology Today Magazine:* *A New Brain Atlas Identifies 100 Brain Regions Never Before Mapped* - Issue date September 8th,

[HCP-Users] Lifespan Pilot Subject Scans

Hello, All. We're interested in examining scans of older (65-75) brains, and as such have great interest in your lifespan study. We understand that it's in the pilot stages, however after examining "The WU-Minn HCP Lifespan Pilot Project" Preliminary report, submitted in Feb. 2015, we see from

[HCP-Users] Palm and Variance

Hello, Is there anyway to include subject-level variance estimates when running palm on a group level? Different subjects in my tfMRI study have different numbers of correct trials modeled in their GLMs, so confidence around each subject's estimate is variable. Seems it would be optimal to

[HCP-Users] Possible Typo in task fmri script

Hello, I was recently adapting some of your great tfMRI analysis pipeline scripts for use with newly collected HCP-compliant data, and I noticed a line that I can't understand. In TaskfMRIAnalysis.v2.0.sh (called by TaskfMRIAnalysis.sh when "new" FSL versions are detected) on line 126 it says:

Re: [HCP-Users] ROIs and Betas from Cifti Data

As an aside, if the end-game of the analysis is a permutation approach (e.g,. PALM) applied to GLM betas, then I wouldn’t expect it to make much difference in terms of power to detect an effect if you parcellate before fitting the Level 1 GLM, or if you simply average the betas from

Re: [HCP-Users] ROIs and Betas from Cifti Data

Thank you for this. We had explored this option in the past and two issues were 1) there was not a parcellation readily available with subcortical structures and 2) I do not feel a need to constrain activation to parcels rather than swaths of signal as they appear to cluster themselves. I'm

Re: [HCP-Users] hcp pipeline problem

It's probably best to post these kinds of questions to the HCP Users list for faster support. Is this happening on clean runs of the latest version of the HCP Pipelines? If so, perhaps posting the output of fslhd on the various input images would reveal the problem. Peace, Matt. From: Sung

Re: [HCP-Users] Same data / Multiple comparisons ?

Dear list, Thanks to all and to you who engaged this puzzling and worrisome topic. I appreciate the pointers to the MegaTrawl and OHBM COBIDAS reports linked in the correspondence below. I agree that it’s not the role of the Human Connectome Project to police the results obtained with the data