Re: [HCP-Users] Best Approach for using old volumetric data to pick parcels-of-interest

Hey Mike, Here's the link to the tools Matt was referring to in the last email. https://edickie.github.io/ciftify I think I'm still a little confused about your exact problem. What do you need to map? Do you already have surfaces for all your participants in GIFTI format? Thanks, Erin On Thu,

Re: [HCP-Users] ROI cluster centers to surface grayordinates

Unfortunately, it is worse than that - even ignoring the individual variability issue (which should not be ignored), a small change in MNI coordinate can jump from one bank of a sulcus to the other, so having only the center coordinate of a cluster makes this a badly posed problem (and thus

Re: [HCP-Users] Best Approach for using old volumetric data to pick parcels-of-interest

The command to use is wb_command -volume-to-surface-mapping, the main surface should generally be the midthickness. Using the -ribbon-constrained method will give you small positive values on the surface when the cortical ribbon just grazes your ROI, so it may be the thing to use (use pial and

Re: [HCP-Users] Error in FreeSurfer processing "recon-all.v6.hires: command not found"

Hi Pubuditha, I'm assuming that you are using the latest release of the HCP Pipelines (v3.25.0). The changes that are causing you a problem are part of those being made as part of conversion to using FreeSurfer version 6. Those changes should not have made it in to a release as of yet. I

[HCP-Users] Error in FreeSurfer processing "recon-all.v6.hires: command not found"

Hi all, I am very new to the HCP pipeline for preprocessing the data and I am trying to adopt to the pipeline. As the first step I am trying the execution of the pipeline with the example data that is given in the tutorial. The first part which is the PreFreeSurfer processing was completed

Re: [HCP-Users] Movement regressor missing

That’s right. To keep the packages smaller we tried not to repeat files. Peace, Matt. From: > on behalf of "Linnman, Clas,Ph.D." > Date: Thursday, March 1,

[HCP-Users] Movement regressor missing

Hi, I downloaded the “resting state fMRI FIX 1 Denoised (Extended)” datasets, but there are no Movement_Regressors.txt included in the unzipped folder. Are these not there for a reason? I can grab them from the other preprocessed datasets, but I was curious as to why they are missing, and if

Re: [HCP-Users] Best Approach for using old volumetric data to pick parcels-of-interest

Hi Tim, Thanks. That’s clear and sounds like a really reasonable approach. Can you point me towards the exact files I’d need to reference and maybe suggest which function calls I’ll need to use to do the volume-to-surface mapping you describe? I’ll whip up a quick script to loop through

Re: [HCP-Users] Correct interpretation of NIH battery test 'Words-in-Noise' in HCP subjects

Hi Robert, Thank you for pointing us to this problem. The HCP Words in Noise score is indeed the NIH Toolbox Words in Noise (WIN) Test computed score, rather than the Toolbox Hearing Threshold Test that was erroneously used for the description in the Data Dictionary. We will fix the data

[HCP-Users] Correct interpretation of NIH battery test 'Words-in-Noise' in HCP subjects

Dear all, we have trouble understanding what the above test actually tests in the context of HCP data. Despite its suggestive name, this test is described (in the updated HCP Data Dictionary and its previous version), as a pure-tone thresholding test that seems to have nothing to do with

[HCP-Users] ROI cluster centers to surface grayordinates

Hi, I have a set of ROI cluster center coordinates in MNI space. My goal is to create similar ROI clusters to use with HCP data. I understand there's no true equivalent in terms of surface grayordinates but what would be the best way to find their approximate position on the surface? Is this the