Re: [HCP-Users] wb_command help
HCP Preprocessing does not include running tractography, and wb_command doesn't do tractography (it can do some specific manipulations of FSL tractography outputs, though, including averaging over ROIs). There are as-yet unsolved issues with tractography (gyral bias, where streamlines prefer to hit at gyral crowns, largely skipping over gyral banks) which makes such comparisons tricky, beyond the conceptual differences of measuring wiring versus measuring co-activation. Tim On Tue, Jun 12, 2018 at 12:35 PM, Rakib Al-Fahad (ralfahad) < ralfa...@memphis.edu> 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 > > > > > > *From: *"Harms, Michael" > *Date: *Tuesday, June 12, 2018 at 12:25 PM > *To: *"Rakib Al-Fahad (ralfahad)" , " > 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 > > > > 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 > <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. > Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > > *From: * on behalf of "Rakib > Al-Fahad (ralfahad)" > *Date: *Tuesday, June 12, 2018 at 11:58 AM > *To: *"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 > > > > > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] wb_command help
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" <mailto:mha...@wustl.edu> Date: Tuesday, June 12, 2018 at 12:25 PM To: "Rakib Al-Fahad (ralfahad)" <mailto:ralfa...@memphis.edu>, "hcp-users@humanconnectome.org"<mailto: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=DwMGaQ=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=7ZVWbrGcEZm19g0l_yR1nELMoFlPJrqV-1SiWrjKVXQ=HexeNxxdshHxMO40Uoy13HksvKyQsQuPXY8jakzSfRA=U-hvh_M_hN-4ljuH8hGM_3aWnnbMrL8anl0_Z9XjI5c=> 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: <mailto:hcp-users-boun...@humanconnectome.org> on behalf of "Rakib Al-Fahad (ralfahad)" <mailto:ralfa...@memphis.edu> Date: Tuesday, June 12, 2018 at 11:58 AM To: "hcp-users@humanconnectome.org"<mailto: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> ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] wb_command help
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 From: "Harms, Michael" Date: Tuesday, June 12, 2018 at 12:25 PM To: "Rakib Al-Fahad (ralfahad)" , "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 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 From: on behalf of "Rakib Al-Fahad (ralfahad)" Date: Tuesday, June 12, 2018 at 11:58 AM To: "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 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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 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 From: on behalf of "Rakib Al-Fahad (ralfahad)" Date: Tuesday, June 12, 2018 at 11:58 AM To: "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 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
