Hi Rakib,

   My colleagues and I normally use the Freesurfer Aseg ROIs and the diffusion 
data in the same T1w folder of the preprocessed HCP data to compute the 
structural connectivity. The same Aseg ROIs in the MNI space can be used for 
functional connectivity.

    To use the HCP1200 parcellation for structural connectivity, I guess you'll 
need to cope with the parcellation defined in grayordinates.

Cheers,
Junyan Wang, Ph.D.
Postdoctoral scholar

USC Stevens Neuroimaging and Informatics Institute
Laboratory of Neuro Imaging (LONI)
Keck School of Medicine of USC
University of Southern California
2025 Zonal Ave.
Los Angeles, CA 90033
Phone: (323) 44-BRAIN (442-7246)
On 06/12/2018 10:35 AM, Rakib Al-Fahad (ralfahad) wrote:
Dr. Michael

ICA based analysis has specific problem. To name a component (ICs), we need 
domain expert. Hence, comparative analysis between structural and functional 
connectivity cannot be quantified. I want to use an atlas template that can 
also be used for DTI based tractographic data. Do I have to use FreeSerfer/FSL 
again to extract ROI based tractographis and time series or wb_command + 
preprocessed HCP data is sufficient? And how to do that?


Thanks

Rakib Al-Fahad
Ph.D. Student
CVPIA Lab
Department of Electrical and Computer Engineering
The University of Memphis
Email: ralfa...@memphis.edu<mailto:ralfa...@memphis.edu>


From: "Harms, Michael" <mha...@wustl.edu><mailto:mha...@wustl.edu>
Date: Tuesday, June 12, 2018 at 12:25 PM
To: "Rakib Al-Fahad (ralfahad)" 
<ralfa...@memphis.edu><mailto:ralfa...@memphis.edu>, 
"hcp-users@humanconnectome.org"<mailto:hcp-users@humanconnectome.org> 
<hcp-users@humanconnectome.org><mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] wb_command help


Hi,
See the "HCP1200 Parcellation+Timeseries+Netmats (PTN)" packages hosted at
https://db.humanconnectome.org/data/projects/HCP_1200<https://urldefense.proofpoint.com/v2/url?u=https-3A__db.humanconnectome.org_data_projects_HCP-5F1200&d=DwMGaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=7ZVWbrGcEZm19g0l_yR1nELMoFlPJrqV-1SiWrjKVXQ&m=HexeNxxdshHxMO40Uoy13HksvKyQsQuPXY8jakzSfRA&s=U-hvh_M_hN-4ljuH8hGM_3aWnnbMrL8anl0_Z9XjI5c&e=>

There are "soft parcellations" (ICA-based, and cortical only) computed at 
dimensionalities of 15, 25, 50, 100, 200, and 300.

Cheers,
-MH

--
Michael Harms, Ph.D.
-----------------------------------------------------------
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.                        Tel: 314-747-6173
St. Louis, MO  63110                          Email: 
mha...@wustl.edu<mailto:mha...@wustl.edu>
From: 
<hcp-users-boun...@humanconnectome.org><mailto:hcp-users-boun...@humanconnectome.org>
 on behalf of "Rakib Al-Fahad (ralfahad)" 
<ralfa...@memphis.edu><mailto:ralfa...@memphis.edu>
Date: Tuesday, June 12, 2018 at 11:58 AM
To: "hcp-users@humanconnectome.org"<mailto:hcp-users@humanconnectome.org> 
<hcp-users@humanconnectome.org><mailto:hcp-users@humanconnectome.org>
Subject: [HCP-Users] wb_command help

Hello,

I am a student of machine learning. I want to study structural and functional 
brain connectivity from HCP data. Is there any way to get ROI based time series 
and structural connectivity using wb_command ? I am not sure about which ROI 
atlas should I use. I need suggestion for specific atlas having 50~100 ROIs.


Thanks

Rakib Al-Fahad
Ph.D. Student
CVPIA Lab
Department of Electrical and Computer Engineering
The University of Memphis
Email: ralfa...@memphis.edu<mailto:ralfa...@memphis.edu>



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