[HCP-Users] freesurferpipeline

Hi, Should I modify the pipeline? Here is my problem, in line 145 of FreeSurferPipeline.sh, it says to call recon-all, but in line 148 there is a pound sign. Should I remove it? Thanks. ___ HCP-Users mailing list HCP-Users@humanconnectome.org

[HCP-Users] lifespan pilot data

Hi, When I use the unprocessed data in SPM, should I uncompress *.gz files first? Additionally, in ../LS2001/unprocessed/3T/T1w_MPR1_Norm/, there are 6 more files than the same directory of other subjects. Why? Thanks. ___ HCP-Users mailing list

[HCP-Users] vertex，parcel

Dear HCP experts, There are WM/GM surface and pial surface. I think vertices and parcels are things to represent these surfaces, but I’m still confused with these two nouns. You know, there is a backtracking algorithm to divide surface into different number of regions with each region having its

[HCP-Users] coordinate of regions

Dear HCP experts, After running preprocess pipeline, I can find the average thickness data of every region for different templates, e.g.,lh.aparc.a2009s.stats, lh.aparc.stats. Where can I find the coordinate of every region, respectively? Thanks. ___

[HCP-Users] regions

Dear experts, After preprocess pipeline, what information can I get from structure MRI, rfMRI, DTI images, except for e.g.,thickness of every region? Thanks. ___ HCP-Users mailing list HCP-Users@humanconnectome.org

[HCP-Users] myelin maps

Hi, I know someone has asked in mail list about extracting average myelin value at ROI level. My command is: ./wb_command -cifti-weighted-stats -roi ./LS2001/MNINonLinear/LS2001.MyelinMap.164k_fs_LR.dscalar.nii Error: cifti-in is missing(No more parameters). How to fix the error? Thanks.

[HCP-Users] PhaseEncodinglist

Hi, This question is small, but I can't find anyone who know it, so I ask you: In process pipeline of lifespan rfMRI data, the PhaseEncodinglist contains phase encoding direction indicators for each corresponding task in the Tasklist. There is a .csv file in data file directory shows "-x", but

[HCP-Users] MTR

Hi, After three parts of structural pipeline, I want to use the image to calculate MTR(magnetization transfer ratio) in SPM using following equation: MTR=100%*(S0-S1)/S0. S0 is the mean signal intensity of a voxel obtained from the sequence using no saturation pulse, and S1 is the mean signal

[HCP-Users] cifti MATLAB

Hi, There's something wrong when I load the cifti dense timeseries file into matlab. >> which ciftiopen /home/Tianjie/cifti/ciftiopen.m >>cii=ciftiopen('/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_stru cture_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_A

[HCP-Users] BOLD signal

Hi, Is there a functional brain region atlas? How can I visualize the BOLD signal of every brain region? Take a step back, is there any way to visualize the signal? Thanks. ___ HCP-Users mailing list HCP-Users@humanconnectome.org

[HCP-Users] GIFTI surface data

Hi, I use the lifespan rfMRI data. After preprocessing, there is a file in /subject/MNINonLinear/Results/rfMRI_REST1_LR named rfMRI_REST1_LR.L.native.func.gii with size, for example, 130576*420. Is this file the cortical BOLD signal time series data? Can I use it to do rfMRI analysis? Thanks.

[HCP-Users] cifti file

Hi, There is a .dtseries.nii file in rfMRI_REST1_LR and the other in rfMRI_REST1_RL, which one should I use? What's the difference? Thanks. ___ HCP-Users mailing list HCP-Users@humanconnectome.org

[HCP-Users] rfMRI BOLD signal

Hi, After I load the .dtseries.nii file to connectome workbench, there is a .dynconn.nii connectivity file, which is not in the directory of the .dtseries.nii file, is the connectivity file generated automatically after I load the CIFTI dense timeseries file? Does the connectivity file shows

[HCP-Users] rfMRI CIFTI

Hi, How to regenerate the two hemispheres' surface timecourses and the parcel-constrained subcortical volume timecourses from the CIFTI dense timeseries using Connectome Workbench's commandline utilities? Thanks. ___ HCP-Users mailing list

[HCP-Users] rfMRI CIFTI

Hi, How to regenerat the two hemispheres' surface timecourses and the parcel-constrained subcortical volume timecourses from the CIFTI dense timeseries using Connectome Workbench's commandline utilities. Thanks. ___ HCP-Users mailing list

[HCP-Users] rfMRI BOLD data

Hi, In HCP Pipelines: fMRISurface part, you said, the surface timeseries from both hemispheres and the subcortical volume timeseries from each subcortical structure are combined in a single data matrix that has the dimensions grayordinates × time. Where can I find the matrix? What’s the file

[HCP-Users] multi-modal parcellation coordinate

Hi, How can I get the coordinates of every region of your multi-modal parcellation? Thanks. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] label map

Hi, I use your multi-modal parcellation,Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_ Group_Colors.32k_fs_LR.dlabel.nii. First ,I use ./wb_command -cifti-convert -to-gifti-ext ./Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Color s.32k_fs_LR.dlabel.nii