Re: [HCP-Users] Statistical comparison of whole brain (surface "voxels" + subcortical / cerebellar voxels) connectivity between two explicitly defined voxels

On Mon, Jul 17, 2017 at 6:21 PM, Regner, Michael < michael.reg...@ucdenver.edu> wrote: > Hello Matt and HCP Community, > > > > Thank you for the helpful e-mail and words of encouragement. We are very > encouraged by the data / results we can view in the Connectome Workbench; > however,

Re: [HCP-Users] Statistical comparison of whole brain (surface "voxels" + subcortical / cerebellar voxels) connectivity between two explicitly defined voxels

Hello Matt and HCP Community, Thank you for the helpful e-mail and words of encouragement. We are very encouraged by the data / results we can view in the Connectome Workbench; however, statistical analysis has proved challenging. Just to reiterate what we are attempting to do: we are hoping

Re: [HCP-Users] mapping HCP data into 7 functional networks (using Thomas Yeo parcellation)

As Matt says, 32k is used to roughly match the acquisition resolution. The 7T data at 1.6mm is on a 59k mesh for the same reasons. If you want to resample them, see the -cifti-resample command (or -metric-resample for a simpler command that does the same surface operation on a different format).

Re: [HCP-Users] mapping HCP data into 7 functional networks (using Thomas Yeo parcellation)

Yes it does seem the first of four columns has 8 distinct numbers. As a side note, is there any released HCP resting state data on a 164k mesh or are they all 32k mesh? Thank you, David Hartman On Mon, Jul 17, 2017 at 6:19 PM, Timothy Coalson wrote: > You can get a text file

Re: [HCP-Users] mapping HCP data into 7 functional networks (using Thomas Yeo parcellation)

Since calling in MATLAB: “ciftiopen('RSN-networks.32k_fs_LR.dlabel.nii', 'workbench\bin_windows64\wb_command.exe')” gives me a matrix with 4 columns whose range is beyond the 17 or 7 corresponding to their functional grouping, I have resorted to using wb-command hoping to get right labelling.

Re: [HCP-Users] mapping HCP data into 7 functional networks (using Thomas Yeo parcellation)

Hi, There are actually 4 different maps in that file. If you load it into Workbench, the name associated with each map tells you what each map is. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental

Re: [HCP-Users] diffusion data merge pipeline

Hi, Is there a particular reason that you can’t provide all the dMRI scans at once, and let the pipeline handle the merging for you? If you process each dMRI run separately, then the individual runs will not be in optimal alignment. (You would be relying on the registration of each run to the

Re: [HCP-Users] diffusion data merge pipeline

I am using the following function (and is looped through the pairs of unique sets of gradient tables (i.e. loops twice for dir99 and dir98): ${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh \ --posData="{posData}" \ --negData="{negData}" \ --path="{path}" \

Re: [HCP-Users] diffusion data merge pipeline

When I run DiffusionPreprocessing, I make the --dwiname=DWIName specific to the diffusion scan (i.e. DWIName= Diffusion_dir-98_run-01) to prevent files from being overwritten. I end up with: ${StudyFolder}/${Subject}/T1w/Diffusion_dir-98_run-01/data.nii.gz

Re: [HCP-Users] diffusion data merge pipeline

Look for the ${StudyFolder}/${Subject}/T1w/Diffusion/data.nii.gz file. Peace, Matt. From: > on behalf of Yeun Kim > Date: Monday, July 17, 2017 at 12:56 PM To:

Re: [HCP-Users] Questions about reconstruction speed of Multi-band EPI sequence in LSCMRR

Hi, You want the high-end recon computer with the GPU. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South