Re: [HCP-Users] CIFTI and NIFTI -parcellating rfMRI

The .nii.gz files are nifti-1 volumes, while the .dtseries.nii files are Cifti files. If you need spatial information, converting Cifti to nifti-1 is not the way to go about it, instead you could use wb_command -cifti-separate into metric (.func.gii, one per hemisphere) and volume files, or use

[HCP-Users] phase encoding and group ICA

Hi all, According to this page http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html, prior to 1 October 2012, the first resting state session of each visit was acquired with RL phase encoding, and the second session was acquired with LR phase encoding (RL/LR). After this

Re: [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

This part of your call: , 'readdata', false); is telling ft_read_cifti to not load the data matrix, that is why it isn't there. If you are just as comfortable in C++, then yes, CiftiLib is likely the best solution, it is directly based on the code we use in connectome workbench for cifti files.

Re: [HCP-Users] phase encoding and group ICA

Why does the order of the individual subject sessions matter for group ICA or PTNs? Peace, Matt. From: > on behalf of Mary Beth > Date: Tuesday, November 24, 2015 at 5:59

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

If you are using -cifti-correlation, there is a -mem-limit option for this purpose, so there isn't a required minimum memory to do it (even in matlab where everything has to be in memory, the 90k x 4.8k timeseries input pales in comparison to the 90k x 90k output). If you are doing everything in

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

I suggested below that Joelle could average Fisher’s z-transformed correlation coefficients (derived from each run within-subject), or treat the multiple runs as within-subjects repeated measures. The idea was that computing correlations between timeseries with 4800 time points will take four

Re: [HCP-Users] phase encoding and group ICA

The subject-specific parcel timeseries were provided in a single text file for each model order with 4800 time points each. I am trying to figure out if time points 2401-3600 from those text files always correspond to the LR session from Day 2, or if they correspond to the RL session from Day 2

Re: [HCP-Users] Is proprietary aspera browser plugin the only way to download the HCP Open data?

Thank you Kevin and Mike! I think I will go with Aspera then. On Tue, Nov 24, 2015 at 11:58 AM, Hodge, Michael wrote: > > > Hi Cherry, > > Because of the size of the data, it really is recommended to use either > the Aspera-based download mechanism via ConnectomeDB, access the

Re: [HCP-Users] phase encoding and group ICA

Hi - Wrt group-ICA, it makes no difference what order the data was fed into the MIGP group-PCA. Wrt the 4 chunks combined into the node timeseries in the 500-subject PTN release: the order is always the following, so you will need to take into account the information you pasted below if you

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

Hi Joelle, In addition to demeaning and possibly variance normalization, it is probably a good idea to detrend each run separately using a linear detrend or a high pass filter before concatenation. (FIX-preprocessed data already includes a 2000s high pass filter.) Another option that is not

Re: [HCP-Users] Tractography on diffusion data for SC matrices

Hi Joelle and all, we have a pipeline that takes diffusion MRI and T1-weighted data as input and automatically computes structural connectivity matrices for arbitrary cortical parcellations using three different connectivity metrics. It also computes functional connectivity matrices from fMRI

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

Hi Greg, Thanks for your response. Indeed, I was considering that myself, to compute the FCs separately and average the LR and RL. Thanks, Joelle On Tue, Nov 24, 2015 at 11:56 AM, Greg Burgess wrote: > Hi Joelle, > > In addition to demeaning and possibly variance

[HCP-Users] CIFTI and NIFTI -parcellating rfMRI

Hi all, I'm working with the 500subjects + MEG2 preprocessed Resting State fMRI 1 Preprocessed dataset. Is the data just standard voxel-wise Nifti (it indeed looks like Nifti-1), or is it in a Cifti format that I need to convert to Nifti? My goal is to parcellate this data into ROI's, and I have

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

Indeed I was assuming you were using FIX cleaned data. I wouldn't recommend not using FIX cleaned data unless you are testing other clean up approaches. Peace, Matt. From: Joelle Zimmermann [joelle.t.zimmerm...@gmail.com] Sent: Tuesday, November 24,

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

Hi Matt, Glad you do point that out, because I was previously looking at the Resting State fMRI 1 Preprocessed, but the Resting State fMRI FIX-Denoised (Compact) is readily available. So I guess for that all I'll need to do is demean and variance normalize, and/or average the two FCs. Thanks,

Re: [HCP-Users] Is proprietary aspera browser plugin the only way to download the HCP Open data?

Hi Cherry, Because of the size of the data, it really is recommended to use either the Aspera-based download mechanism via ConnectomeDB, access the data via Amazon S3 (https://wiki.humanconnectome.org/display/PublicData/Connecting+to+Connectome+Data+via+AWS), or via Connectome-in-a-Box

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

It’s less RAM-intensive since you only need to load one timeseries at a time. --Greg Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

I think maybe we need to be explicit about exactly what we're talking about averaging? Cheers. Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford. OX3 9 DU, UK +44 (0) 1865 222726

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

2 dconns instead of one? Sent from my Verizon Wireless 4G LTE smartphone Original message From: Greg Burgess Date: 11/24/2015 1:03 PM (GMT-06:00) To: "Glasser, Matthew" Cc: Joelle Zimmermann , "Elam,

Re: [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

Hello, With fieldTrip reading using this line mycifti = ft_read_cifti( '/Users/David/Desktop/HumanConnectomeProject/HCP_S500_R468_rfMRI_MIGP_d4500ROW_zcorr/HCP_S500_R468_MIGPd4500ROW.dconn.nii', 'readdata', false); I get: dimond (pos_pos), hdr (1x1 struct), unit ('mm'), brain structure,

Re: [HCP-Users] Is proprietary aspera browser plugin the only way to download the HCP Open data?

Hi, Cherry, As far as I know, the fastest way to download HCP data is still through the Aspera client (unless you’re doing your computing on Amazon AWS, see below). The best guide to this would be the Python tutorial here:

Re: [HCP-Users] Tractography on diffusion data for SC matrices

Hi Jennifer, That's good to hear! I don't have much experience with tractography, but it looks like bedpostX creates all the files you need for running probabilistic tractography (probabilistic tractography itself is run with probtrackX for example). I suppose the probabilistic tractography is