[HCP-Users] Infinite values in Group average data

I downloaded group average functional correlation file: HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii Some diagonal elements of the square matrix (91282x91282) are infinite (Please see below). I want to use this matrix in ananalysis; however, I am not sure how to understand or deal

[HCP-Users] Subjects who have 7T acquired

Hello, I read that out of the 1200 subjects, 184 have 7T data acquired in addition to 3T. I tried searching for more information on these 184 but couldn't find any. Is there any information about their subject IDs or is manually sifting through each one of them the only way to know which subjects

Re: [HCP-Users] Clarification request for data codes

Hi Brittany, Sorry for the confusion. The codes for the "Menstrual_CycleLength", Average length of participant's menstrual cycles in days data are 1=Less than 25 days, 2=Between 25-35 days, and 3=More than every 35 days. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome

[HCP-Users] Problem regarding to mount 1200-release data to NITRIC-CE

Dear hcp teams， I sorry to bother you again with same problem. I used default options and mounted data successfully. But when I checked /s3/hcp, I found that data in it has only 900 subjects. Obviously, it's not the latest 1200-release data. Since I want to analyse the latest version of

[HCP-Users] Parcellation of subcortical areas

Hello, I have been using wb_command -cifti-parcellate to extract time series using Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii (and R) For subcortical areas, I see the border files, but not the dlabel.nii files on https://balsa.wustl.edu/study/show/RVVG. Can

Re: [HCP-Users] Problem regarding to mount 1200-release data to NITRIC-CE

On Mon, May 15, 2017 at 8:48 AM, Irisqql0922 wrote: > ... > I use command: > : > ~/.passwd-s3fs > If this is really the command you used, then it wouldn't work: you need "echo" at the start of it, like this: echo : > ~/.passwd-s3fs Please look at the file's contents with

Re: [HCP-Users] Parcellation of subcortical areas

The HCP-MMP1.0 does not contain subcortical parcellations. This would be future work. Others may be able to point you to some cerebellum/subcortical parcellations from other works. As for "borders": subcortical areas, which are represented as volume-based structures, cannot have their

Re: [HCP-Users] Infinite values in Group average data

Per the name "zcorr", the correlation values have been z-transformed (fisher's small z transform). I am somewhat confused as to why some elements in the diagonal are not infinite. The "true" value of applying this transform would be infinite on the entire diagonal, as arctanh(1) is infinite. I

[HCP-Users] Reminder to Register for HCP Course 2017

Only a few spaces remain for the 2017 HCP Course: "Exploring the Human Connectome". For more info and to register: https://store.humanconnectome.org/courses/2017/exploring-the-human-connectome.php Don't forget to also reserve your accommodation for the course by May 17, 2017 to be sure of

Re: [HCP-Users] Problem regarding to mount 1200-release data to NITRIC-CE

Dear Qinqin Li, Based on my checking so far, AWS credentials that give you access to the HCP_900 section of the S3 bucket should also give you access to the HCP_1200 section of the bucket. One thing I would suggest is to go back to using the mount point provided by the NITRC-CE-HCP

Re: [HCP-Users] task fMRI analysis

Hi, I’m not sure what to make of those errors, but if the design.fsf doesn’t work with FEAT, that suggests that something is wrong with it. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders

Re: [HCP-Users] Infinite values in Group average data

Thank you for the response. I am, too, confused by some being non-zero finite values, and others being infinities. Before computing a correlation matrix, if standardized by subtracting the mean and scaling by variance, all diagonal elements should be exactly 1. What I am concerned about is how

[HCP-Users] Regression of Physiological Noise -- updates?

Hi all Correct me if I'm wrong, but I believe that the HCP data has not yet had physiological noise regressed out. From previous threads, it seems the general consensus was that implementing this capability was being worked on. Can we expect a Connectome Workbench tool for this any time soon?

Re: [HCP-Users] Regression of Physiological Noise -- updates?

Some physiological noise is regressed out through the ICA+FIX cleanup (where it is part of the noise components). What is not regressed out is the global physiological noise, e.g. related to respiration. We are indeed working on a method for doing this in a data-driven (as opposed to using

Re: [HCP-Users] Infinite values in Group average data

Right. Peace, Matt. From: > on behalf of Sang-Yun Oh > Date: Tuesday, May 16, 2017 at 11:25 AM To: Timothy Coalson > Cc:

Re: [HCP-Users] Infinite values in Group average data

This makes more sense! Sorry I missed your mention of fisher-z transform So I would apply tanh to each element to revert back to regular correlation coefficients Thank you for your help! Best, Sang On Mon, May 15, 2017 at 5:57 PM Timothy Coalson wrote: > After the fisher-z

Re: [HCP-Users] Infinite values in Group average data

I am also finding that some off-diagonal elements in this matrix are also greater than 1 indicating this matrix is not a correlation matrix. In [5]: img Out[5]: memmap([[ 8.66434002e+00, 1.96847185e-01, 1.66294336e-01, ..., 1.01449557e-01, 7.45474100e-02, 1.15624115e-01],

Re: [HCP-Users] Parcellation of subcortical areas

There are a variety of subcortical parcellations out there including these: https://surfer.nmr.mgh.harvard.edu/fswiki/StriatumParcellation_Choi2012 http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011 These were made with a very different approach than the HCP’s multi-modal

Re: [HCP-Users] Infinite values in Group average data

After the fisher-z transform, you can have values greater than 1, see the graph on the right: https://en.wikipedia.org/wiki/Fisher_transformation This is why the "correct" answer for the diagonal is infinity for the "zcorr" file. Tim On Mon, May 15, 2017 at 7:51 PM, Sang-Yun Oh

Re: [HCP-Users] Problem regarding to mount 1200-release data to NITRIC-CE

Dear Qinqin Li, First of all, you are correct that in using the latest version of the NITRC-CE for HCP, the 900 subjects release is mounted at /s3/hcp. We just recently got the data from the 1200 subjects release fully uploaded to the S3 bucket. I am working with the NITRC folks to get the

Re: [HCP-Users] Problem regarding to mount 1200-release data to NITRIC-CE

Hi Tim, I am glad to do the test, and I will let you how it goes :) Best, Qinqin Li On 05/15/2017 23:07，Timothy B. Brown wrote： Dear Qinqin Li, First of all, you are correct that in using the latest version of the NITRC-CE for HCP, the 900 subjects release is mounted