[HCP-Users] Mean scalar values over parcellated regions

[Cook, Philip]

Hi,

I would like to produce a text file with the mean values of thickness, myelin 
etc over the parcellated regions provided in the HCP preprocessing pipeline 
output, specifically those listed in the  ".aparc.164k_fs_LR.dlabel.nii" file. 
I managed a single ROI I think, with

 wb_command \
   -cifti-label-to-roi 130004_MR1.aparc.164k_fs_LR.dlabel.nii \
   /tmp/roi.dscalar.nii \
   -key 44

and then 

 wb_command \
  -cifti-weighted-stats 130004_MR1.SmoothedMyelinMap_BC.164k_fs_LR.dscalar.nii \
  -spatial-weights \
  -left-area-metric 130004_MR1.L.SmoothedMyelinMap_BC.164k_fs_LR.func.gii \
  -right-area-metric 130004_MR1.R.SmoothedMyelinMap_BC.164k_fs_LR.func.gii \
  -mean \
  -roi /tmp/roi.dscalar.nii 

Is there a way to do this for all of the ROIs in one pass? 


Thanks
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Re: [HCP-Users] Optical head tracking data?

[Jon Houck]

Thank you -- that's good to know.

Jon



On Thu, Mar 22, 2018 at 11:14 AM, Glasser, Matthew 
wrote:

> I don’t think this actually ended up being recorded unfortunately.  The
> motion camera ended up not being very reliable, with motion from the skin
> on the face where a sensor was adhered interacting with these results.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Jon Houck <
> jho...@unm.edu>
> Date: Thursday, March 22, 2018 at 12:07 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Optical head tracking data?
>
> Hello,
>
> I noticed in the release manuals that although during fMRI  head motion
> data is collected from the Kineticor system, the motion parameters used in
> preprocessing (Movement_Regressors.txt, etc. ) are based on the
> transformation to the SBRef image.  I couldn’t find the moire phase tracker
> camera output listed in release appendix III, which is otherwise pretty
> exhaustive.  Could someone please point me to the positional information
> files?  I've searched the website and documentation, but it's entirely
> possible that I missed something or used the wrong search terms.
>
> Thank you,
>
> Jon
>
>
>
>
>
> --
> Jon M. Houck, Ph.D.
> Research Assistant Professor
> Department of Psychology
> Center on Alcoholism, Substance Abuse, and Addictions
> University of New Mexico
> Albuquerque, NM 87131
> http://casaa.unm.edu/jhouck.html
>
> ___
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>

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Re: [HCP-Users] Optical head tracking data?

[Glasser, Matthew]

I don’t think this actually ended up being recorded unfortunately.  The motion 
camera ended up not being very reliable, with motion from the skin on the face 
where a sensor was adhered interacting with these results.

Peace,

Matt.

From: 
>
 on behalf of Jon Houck >
Date: Thursday, March 22, 2018 at 12:07 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Optical head tracking data?

Hello,

I noticed in the release manuals that although during fMRI  head motion data is 
collected from the Kineticor system, the motion parameters used in 
preprocessing (Movement_Regressors.txt, etc. ) are based on the transformation 
to the SBRef image.  I couldn’t find the moire phase tracker camera output 
listed in release appendix III, which is otherwise pretty exhaustive.  Could 
someone please point me to the positional information files?  I've searched the 
website and documentation, but it's entirely possible that I missed something 
or used the wrong search terms.

Thank you,

Jon





--
Jon M. Houck, Ph.D.
Research Assistant Professor
Department of Psychology
Center on Alcoholism, Substance Abuse, and Addictions
University of New Mexico
Albuquerque, NM 87131
http://casaa.unm.edu/jhouck.html

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[HCP-Users] Optical head tracking data?

[Jon Houck]

 Hello,

I noticed in the release manuals that although during fMRI head motion data
is collected from the Kineticor system, the motion parameters used in
preprocessing (Movement_Regressors.txt, etc. ) are based on the
transformation to the SBRef image.  I couldn’t find the moire phase tracker
camera output listed in release appendix III, which is otherwise pretty
exhaustive.  Could someone please point me to the positional information
files?  I've searched the website and documentation, but it's entirely
possible that I missed something or used the wrong search terms.

Thank you,

Jon






-- 
Jon M. Houck, Ph.D.
Research Assistant Professor
Department of Psychology
Center on Alcoholism, Substance Abuse, and Addictions
University of New Mexico
Albuquerque, NM 87131
http://casaa.unm.edu/jhouck.html

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[HCP-Users] Optical head tracking data?

[Jon Houck]

Hello,

I noticed in the release manuals that although during fMRI  head motion
data is collected from the Kineticor system, the motion parameters used in
preprocessing (Movement_Regressors.txt, etc. ) are based on the
transformation to the SBRef image.  I couldn’t find the moire phase tracker
camera output listed in release appendix III, which is otherwise pretty
exhaustive.  Could someone please point me to the positional information
files?  I've searched the website and documentation, but it's entirely
possible that I missed something or used the wrong search terms.

Thank you,

Jon





-- 
Jon M. Houck, Ph.D.
Research Assistant Professor
Department of Psychology
Center on Alcoholism, Substance Abuse, and Addictions
University of New Mexico
Albuquerque, NM 87131
http://casaa.unm.edu/jhouck.html

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Re: [HCP-Users] FW: asking for one method to combine LR.nii and RL.nii of dMRI or fMRI data of HCP lifespan pilot 1a

[Elam, Jennifer]

We are not planning to have an initial Lifespan data release until sometime in 
the first half of 2019.


Best,

Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Glasser, Matthew 

Sent: Thursday, March 22, 2018 10:17:18 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] FW: asking for one method to combine LR.nii and RL.nii of 
dMRI or fMRI data of HCP lifespan pilot 1a

I am not sure on the timetable, but perhaps someone else can comment.

Peace,

Matt.

From: 张辉 >
Date: Thursday, March 22, 2018 at 10:14 AM
To: Matt Glasser >
Subject: Re:Re: [HCP-Users] asking for one method to combine LR.nii and RL.nii 
of dMRI or fMRI data of HCP lifespan pilot 1a

 Dear Matt
   I have been excited to receive your email. Could I inquire the schedule 
time-table for the lifespan data release of preprocessed data?

Extend greeting!

Zhanghui




At 2018-03-22 22:26:16, "Glasser, Matthew" 
> wrote:
Did you try running the HCP Pipelines on the data?  This will handle the 
combination for dMRI.  For fMRI the data can be combined after sICA+FIX cleanup 
after demeaning (and perhaps variance normalizing) it.  Given that you may not 
wish to deal with preprocessing the lifespan pilot data, you might be better 
off exploring your hypothesis in the already preprocessed young adult HCP data 
and waiting for the lifespan data release of preprocessed data.

Peace,

Matt.

From: 
>
 on behalf of 张辉 >
Date: Thursday, March 22, 2018 at 9:13 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] asking for one method to combine LR.nii and RL.nii of dMRI 
or fMRI data of HCP lifespan pilot 1a


Dear Sir



I’m a pediatric neurosurgeon from Guangzhou China. For testing my hypothesis 
inspireed by pediatric neurosurgery practice, I attempt to use the data of HCP 
lifespan pilot 1a to expore the function of some brain region. Although I spent 
about several monthes searching the solution for combining LR.nii and RL.nii of 
dMRI or fMRI data, I find I can’t do it. Could you please send me the solution 
you recommend? Thank you very much!





Best regards, and to my





Zhang hui



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[HCP-Users] FW: asking for one method to combine LR.nii and RL.nii of dMRI or fMRI data of HCP lifespan pilot 1a

[Glasser, Matthew]

I am not sure on the timetable, but perhaps someone else can comment.

Peace,

Matt.

From: 张辉 >
Date: Thursday, March 22, 2018 at 10:14 AM
To: Matt Glasser >
Subject: Re:Re: [HCP-Users] asking for one method to combine LR.nii and RL.nii 
of dMRI or fMRI data of HCP lifespan pilot 1a

 Dear Matt
   I have been excited to receive your email. Could I inquire the schedule 
time-table for the lifespan data release of preprocessed data?

Extend greeting!

Zhanghui




At 2018-03-22 22:26:16, "Glasser, Matthew" 
> wrote:
Did you try running the HCP Pipelines on the data?  This will handle the 
combination for dMRI.  For fMRI the data can be combined after sICA+FIX cleanup 
after demeaning (and perhaps variance normalizing) it.  Given that you may not 
wish to deal with preprocessing the lifespan pilot data, you might be better 
off exploring your hypothesis in the already preprocessed young adult HCP data 
and waiting for the lifespan data release of preprocessed data.

Peace,

Matt.

From: 
>
 on behalf of 张辉 >
Date: Thursday, March 22, 2018 at 9:13 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] asking for one method to combine LR.nii and RL.nii of dMRI 
or fMRI data of HCP lifespan pilot 1a

Dear Sir

I’m a pediatric neurosurgeon from Guangzhou China. For testing my hypothesis 
inspireed by pediatric neurosurgery practice, I attempt to use the data of HCP 
lifespan pilot 1a to expore the function of some brain region. Although I spent 
about several monthes searching the solution for combining LR.nii and RL.nii of 
dMRI or fMRI data, I find I can’t do it. Could you please send me the solution 
you recommend? Thank you very much!


Best regards, and to my


Zhang hui

发送自 Windows 10 版邮件应用


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Re: [HCP-Users] asking for one method to combine LR.nii and RL.nii of dMRI or fMRI data of HCP lifespan pilot 1a

[Glasser, Matthew]

Did you try running the HCP Pipelines on the data?  This will handle the 
combination for dMRI.  For fMRI the data can be combined after sICA+FIX cleanup 
after demeaning (and perhaps variance normalizing) it.  Given that you may not 
wish to deal with preprocessing the lifespan pilot data, you might be better 
off exploring your hypothesis in the already preprocessed young adult HCP data 
and waiting for the lifespan data release of preprocessed data.

Peace,

Matt.

From: 
>
 on behalf of 张辉 >
Date: Thursday, March 22, 2018 at 9:13 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] asking for one method to combine LR.nii and RL.nii of dMRI 
or fMRI data of HCP lifespan pilot 1a

Dear Sir

I’m a pediatric neurosurgeon from Guangzhou China. For testing my hypothesis 
inspireed by pediatric neurosurgery practice, I attempt to use the data of HCP 
lifespan pilot 1a to expore the function of some brain region. Although I spent 
about several monthes searching the solution for combining LR.nii and RL.nii of 
dMRI or fMRI data, I find I can’t do it. Could you please send me the solution 
you recommend? Thank you very much!


Best regards, and to my


Zhang hui

发送自 Windows 10 版邮件应用


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[HCP-Users] asking for one method to combine LR.nii and RL.nii of dMRI or fMRI data of HCP lifespan pilot 1a

[张辉]

Dear Sir

I’m a pediatric neurosurgeon from Guangzhou China. For testing my hypothesis 
inspireed by pediatric neurosurgery practice, I attempt to use the data of HCP 
lifespan pilot 1a to expore the function of some brain region. Although I spent 
about several monthes searching the solution for combining LR.nii and RL.nii of 
dMRI or fMRI data, I find I can’t do it. Could you please send me the solution 
you recommend? Thank you very much!


Best regards, and to my 


Zhang hui

发送自 Windows 10 版邮件应用


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[HCP-Users] problems about fibre tracking between surface ROIs

[Xinyang Liu]

Dear HCP experts,


Hi. We just started to learn tractography between functional ROIs and met some 
problems. Our purpose is to do fibre-tracing between face-related functional 
ROIs. We got the surface ROIs (.func.gii) with HCP fMRI data and Glasser MMP 
atlas. However, in our initial try of fibre tracing, there was no streamline 
coming out from the seed ROI. Our seed and target ROIs were separately the FFA 
and OFA surface regions in the right hemisphere.


Our command was:
probtrackx2 -x /.../100307_thickness_analysis_ROI_FFA/R.2stat.func.gii 
--seedref=/.../100307/T1w/Diffusion/B0_brain.nii.gz -l -c 0.2 -S 2000 
--steplength=0.5 -P 5000 --meshspace=caret --forcedir --opd -s 
/.../100307/T1w/Diffusion.bedpostX/merged -m 
/.../100307/T1w/Diffusion.bedpostX/nodif_brain_mask 
--dir=/.../face_network_tracking/output/output1 
--waypoints=/.../100307_thickness_analysis_ROI_OFA_R/R.2stat.func.gii -o 
FFAtoOFA


The output waytotal is 0 and the fdt_path image is empty.


My questions are as follows:
1. Why there was no streamline coming out from the seed surface ROI?
2. Is it better that we change the surface ROI to volume ROI? If so, how to 
acquire the cortical functional volume ROI with HCP data?
3. The FSL says that it now accepts surface data, does it mean we don't need to 
do transfer between surface and diffusion space and then set parameters like 
--xmf, --meshspace and --seedref?


Any guidance would be very appreciated.


Best regards,
Xinyang Liu




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