[HCP-Users] Physiological Signals,

Hi everybody, I am trying to remove physiological noise using RETROICOR and data provided on "rfMRI_REST1_LR_Physio_log.txt" files for each subject. According to HCP tutorial the second column in these files corresponds to cardiac signal(pulse oximetry). If I plot the column, simple visual analy

[HCP-Users] MMP-1.0 parcellation

Hi all, I would like to see MMP-1.0 parcellation on a specific HCP subject native T1 surface. What is the best files or/and methods to do so? I appreciate any pointers regarding this. Many thanks, Kamal ___ HCP-Users mailing list HCP-Users@humanconnec

[HCP-Users] MMP1.0 surface label ROIs in a subject T1w space

Hi all, I need to see the MMP1.0 ROIs in volume format on subject T1w native space. I am using following command to convert surface ROIs to volume ROIs in a subject T1w space: wb_command -label-to-volume-mapping -nearest-vertex x I use following arguments: = {Subject}/T1w/fsaverage_LR3

Re: [HCP-Users] Problem loading a single surface ROI with wb_view

Hi Tim, Is this type of file OK though for seeding in FSL probtrackx? Many thanks for your response, Kamal. From: Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday, October 27, 2016 at 2:35 PM To: "Shadi, Kamal" mailto:kamal.shad...@gatech.edu>> Cc: "hc

[HCP-Users] FNIRT for HCP diffusion data

Hi all, I am trying to run probtrackx using HCP preprocessed diffusion data and MMP1.0 ROIs. To my understanding the corresponding T1w image of MMP1.0 ROIs is: HCP_PhaseTwo / Q1-Q6_RelatedParcellation210 / MNINonLinear / Q1-Q6_RelatedParcellation210_AverageT1w_restore.nii.gz Is this a right cho

Re: [HCP-Users] FNIRT for HCP diffusion data

Hi Matt., Yes, It is an HCP subject. Thanks, Kamal From: "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Tuesday, November 1, 2016 at 7:25 PM To: "Shadi, Kamal" mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users

Re: [HCP-Users] FNIRT for HCP diffusion data

file HCP releases to be used by FNIRT? From: "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Tuesday, November 1, 2016 at 7:29 PM To: "Shadi, Kamal" mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org

Re: [HCP-Users] FNIRT for HCP diffusion data

—xfm arguments of probtrackx? From: "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Tuesday, November 1, 2016 at 7:41 PM To: "Shadi, Kamal" mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"

Re: [HCP-Users] FNIRT for HCP diffusion data

2, 2016 at 2:30 PM To: "Shadi, Kamal" mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] FNIRT for HCP diffusion data No need for XFMs.

[HCP-Users] physical adjacency of MMP1.0 ROIs

Hi all, How can I test if two MMP1.0 ROIs are physically adjacent? Is there a way to do this by web_command? Thanks, Kamal ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] gif surface to obj

Hi all, Does human connectome workbench have a tool to convert gii surfaces to obj? Thanks, Kamal ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] border file

Hi All, It seems that each vertex in the border files has an associated weight. What is this weight? If I want to draw a border vertex by vertex, how should I use the weights? Thanks, Kamal ___ HCP-Users mailing list HCP-Users@humanconnectome.org htt

[HCP-Users] pconn cifti files in ASCII

Hi all, Is there anyway I can get the pconn cifti files in ASCII format? Thanks, Kamal ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] wbsparse

Hi All, Is there anyway I can use trajTemp.wbsparse file to extract connectivity information between a vertex on a surface and an ROI in gift label file (streamline count in particular)? The information of trajTemp file is as follows: Name: pm1.trajTEMP.wbsparse T

Re: [HCP-Users] wbsparse

Yes, It’s in https://balsa.wustl.edu/study/show/W336. From: "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Wednesday, February 28, 2018 at 5:28 PM To: "Shadi, Kamal" mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users

Re: [HCP-Users] wbsparse

>> Date: Wednesday, February 28, 2018 at 6:56 PM To: "Glasser, Matthew" mailto:glass...@wustl.edu>> Cc: "Shadi, Kamal" mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@h

[HCP-Users] Structural connectivity matrix

Hello HCP experts, Is there any structural connectivity matrix available for HCP subjects on the MMP parcellation? Regards, Kamal ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] BedpostX for 7T Diffusion data

Dear HCP experts, Is bedpostx data available for 7T dMRI scans? Regards, Kamal ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] MMP parcellation for 7T

Dear HCP Experts, Is there a dlabel.nii file containing 180 MMP ROIs per hemisphere for 7T data release? I can find the file for 3T release in BALSA (Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii) but I could not find the similar file for 7T? Thanks in advance, K

[HCP-Users] MMP parcellation for 7T

Dear HCP experts, Is there a dlabel.nii file containing 180 MMP ROIs per hemisphere for 7T data release? I can find the file for 3T release in BALSA (Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii) but I could not find the similar file for 7T? Regards, Kamal