Re: [HCP-Users] Motor task contrats: no RH-cue, LH-cue, etc.?

2017-02-09 Thread Burgess, Gregory 
Yes, I believe that would yield the correct Cohen’s d.
--Greg


Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Psychiatry
Phone: 314-362-7864
Email: gburg...@wustl.edu

> On Feb 7, 2017, at 12:12 PM, Xavier Guell Paradis  wrote:
>
> Hi Greg,
> Thank you for your reply. Would you recommend the following commands to 
> analyze the data as you suggested?:
>
> 1) -cifti-merge all level2 cope files of RH (create 
> "mergedcopeMOTORRHONLY.dtseries.nii")
>
> 2) -cifti-merge all level2 cope files of CUE (create 
> "mergedcopeMOTORCUEONLY.dtseries.nii")
>
> 3) calculate RH minus CUE cope file as follows:
> -cifti-math '(x) - (y)' /mergedcopeMOTORRHMINUSCUE.dtseries.nii -var x 
> /mergedcopeMOTORRHONLY.dtseries.nii -var y 
> /mergedcopeMOTORCUEONLY.dtseries.nii
>
> 4) then obtain Cohen's d as follows:
> -cifti-reduce /mergedcopeMOTORTMINUSCUE.dtseries.nii MEAN 
> /meancopeMOTORTMINUSCUE.dscalar.nii;
> -cifti-reduce /mergedcopeMOTORHMINUSCUE.dtseries.nii STDEV 
> /stdevcopeMOTORTMINUSCUE.dscalar.nii;
> -cifti-math '(mean) / stdev' /cohendmapMOTORTMINUSCUE.dscalar.nii -var mean 
> /meancopeMOTORTMINUSCUE.dscalar.nii -var stdev 
> /stdevcopeMOTORTMINUSCUE.dscalar.nii
>
> Thank you very much,
> Xavier.
> 
> From: Burgess, Gregory [gburg...@wustl.edu]
> Sent: Monday, February 06, 2017 5:18 PM
> To: Xavier Guell Paradis
> Cc: hcp-users@humanconnectome.org
> Subject: Re: [HCP-Users] Motor task contrats: no RH-cue, LH-cue, etc.?
>
> I thought that contrasting each effector against the average of the others 
> (e.g., RH-AVG) was a more-effective control to isolate motor-specific 
> regions. If you are still interested in contrasting each effector versus the 
> cue (controlling for visual activation without controlling for other 
> task-related processes), it is possible for you to create it yourself by 
> subtracting the cope maps for ‘CUE’ from the cope for each effector.
>
> --Greg
>
> 
> Greg Burgess, Ph.D.
> Staff Scientist, Human Connectome Project
> Washington University School of Medicine
> Department of Psychiatry
> Phone: 314-362-7864
> Email: gburg...@wustl.edu
>
>> On Feb 3, 2017, at 4:25 PM, Xavier Guell Paradis  wrote:
>>
>> Dear HCP experts,
>> I was wondering if there is any reason why motor contrasts of one motor task 
>> minus cue (e.g. RH-Cue) were not calculated.
>> Thank you very much,
>> Xavier.
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>
> 
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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 
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[HCP-Users] aws cp failed

2017-02-09 Thread Kevin LARCHER 
Hi to all,
I got issues to download specific files from the amazon S3 cloud. It seems
that the files are inconsistently not accessible.
Here are the command lines I tried :

aws s3 ls s3://hcp-openaccess/HCP_900/100307/MNINonLinear/
   PRE Native/
   PRE ROIs/
   PRE Results/
   PRE fsaverage_LR32k/
   PRE xfms/
2016-02-08 14:49:36   4245 100307.164k_fs_LR.wb.spec
2016-02-08 14:49:373386464
100307.ArealDistortion_FS.164k_fs_LR.dscalar.nii
2016-02-08 14:49:373096548
100307.ArealDistortion_MSMAll.164k_fs_LR.dscalar.nii
2016-02-08 14:49:383386464
100307.ArealDistortion_MSMSulc.164k_fs_LR.dscalar.nii
2016-02-08 14:49:383090164 100307.BA.164k_fs_LR.dlabel.nii
2016-02-08 14:49:383096548
100307.EdgeDistortion_MSMAll.164k_fs_LR.dscalar.nii
2016-02-08 14:49:39 815827
100307.L.ArealDistortion_FS.164k_fs_LR.shape.gii
2016-02-08 14:49:39 809681
100307.L.ArealDistortion_MSMSulc.164k_fs_LR.shape.gii
2016-02-08 14:49:39  13908 100307.L.BA.164k_fs_LR.label.gii
2016-02-08 14:49:39 674153 100307.L.MyelinMap.164k_fs_LR.func.gii
2016-02-08 14:49:40 665083 100307.L.MyelinMap_BC.164k_fs_LR.func.gii
2016-02-08 14:49:40 648258 100307.L.RefMyelinMap.164k_fs_LR.func.gii
2016-02-08 14:49:40 669729
100307.L.SmoothedMyelinMap.164k_fs_LR.func.gii
2016-02-08 14:49:40 661355
100307.L.SmoothedMyelinMap_BC.164k_fs_LR.func.gii
2016-02-08 14:49:40  18966 100307.L.aparc.164k_fs_LR.label.gii
2016-02-08 14:49:41  29305 100307.L.aparc.a2009s.164k_fs_LR.label.gii
2016-02-08 14:49:41   4789 100307.L.atlasroi.164k_fs_LR.shape.gii
2016-02-08 14:49:41 687558 100307.L.corrThickness.164k_fs_LR.shape.gii
2016-02-08 14:49:41 742247 100307.L.curvature.164k_fs_LR.shape.gii
2016-02-08 14:49:412651457 100307.L.flat.164k_fs_LR.surf.gii
2016-02-08 14:49:423635412 100307.L.inflated.164k_fs_LR.surf.gii
2016-02-08 14:49:423633563 100307.L.inflated_MSMAll.164k_fs_LR.surf.gii
2016-02-08 14:49:423640854 100307.L.midthickness.164k_fs_LR.surf.gii
2016-02-08 14:49:433640040
100307.L.midthickness_MSMAll.164k_fs_LR.surf.gii
2016-02-08 14:49:433643610 100307.L.pial.164k_fs_LR.surf.gii
2016-02-08 14:49:433642908 100307.L.pial_MSMAll.164k_fs_LR.surf.gii
2016-02-08 14:49:44 808655 100307.L.refsulc.164k_fs_LR.shape.gii
2016-02-08 14:49:443614784 100307.L.sphere.164k_fs_LR.surf.gii
2016-02-08 14:49:45 811941 100307.L.sulc.164k_fs_LR.shape.gii
2016-02-08 14:49:45 689770 100307.L.thickness.164k_fs_LR.shape.gii
2016-02-08 14:49:463633792 100307.L.very_inflated.164k_fs_LR.surf.gii
2016-02-08 14:49:463631135
100307.L.very_inflated_MSMAll.164k_fs_LR.surf.gii
2016-02-08 14:49:463640169 100307.L.white.164k_fs_LR.surf.gii
2016-02-08 14:49:473638847 100307.L.white_MSMAll.164k_fs_LR.surf.gii
2016-02-08 14:49:47   3837 100307.MSMAll.164k_fs_LR.wb.spec
2016-02-08 14:49:473090100 100307.MyelinMap.164k_fs_LR.dscalar.nii
2016-02-08 14:49:483090100 100307.MyelinMap_BC.164k_fs_LR.dscalar.nii
2016-02-08 14:49:483096388
100307.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii
2016-02-08 14:49:48 814380
100307.R.ArealDistortion_FS.164k_fs_LR.shape.gii
2016-02-08 14:49:48 804430
100307.R.ArealDistortion_MSMSulc.164k_fs_LR.shape.gii
2016-02-08 14:49:50  14113 100307.R.BA.164k_fs_LR.label.gii
2016-02-08 14:49:50 673838 100307.R.MyelinMap.164k_fs_LR.func.gii
2016-02-08 14:49:50 665112 100307.R.MyelinMap_BC.164k_fs_LR.func.gii
2016-02-08 14:49:51 648611 100307.R.RefMyelinMap.164k_fs_LR.func.gii
2016-02-08 14:49:51 669614
100307.R.SmoothedMyelinMap.164k_fs_LR.func.gii
2016-02-08 14:49:51 661316
100307.R.SmoothedMyelinMap_BC.164k_fs_LR.func.gii
2016-02-08 14:49:51  18943 100307.R.aparc.164k_fs_LR.label.gii
2016-02-08 14:49:52  29394 100307.R.aparc.a2009s.164k_fs_LR.label.gii
2016-02-08 14:49:52   4850 100307.R.atlasroi.164k_fs_LR.shape.gii
2016-02-08 14:49:52 686967 100307.R.corrThickness.164k_fs_LR.shape.gii
2016-02-08 14:49:52 742148 100307.R.curvature.164k_fs_LR.shape.gii
2016-02-08 14:49:522541434 100307.R.flat.164k_fs_LR.surf.gii
2016-02-08 14:49:533510625 100307.R.inflated.164k_fs_LR.surf.gii
2016-02-08 14:49:533509516 100307.R.inflated_MSMAll.164k_fs_LR.surf.gii
2016-02-08 14:49:533515499 100307.R.midthickness.164k_fs_LR.surf.gii
2016-02-08 14:49:543515737
100307.R.midthickness_MSMAll.164k_fs_LR.surf.gii
2016-02-08 14:49:553517583 100307.R.pial.164k_fs_LR.surf.gii
2016-02-08 14:49:553517793 100307.R.pial_MSMAll.164k_fs_LR.surf.gii
2016-02-08 14:49:56 808740 100307.R.refsulc.164k_fs_LR.shape.gii
2016-02-08 14:49:563492005 100307.R.sphere.164k_fs_LR.surf.gii
2016-02-08 14:49:56 811590 100307.R.sulc.164k_fs_LR.shape.gii
2016-02-08 14:49:57 689275 100307.R.thickness.164k_fs_LR.shape.gii
2016-02-08 14:49:573508069

Re: [HCP-Users] Calculating cross-frequency power envelope correlations with HCP MEG dataset

2017-02-09 Thread Georgios Michalareas 

Dear Olu,

in source level we only have released power time-series. So if you want 
to correlate high frequency power to low frequency phase , then you 
cannot do this with the released source level time-series. In this case 
you would need to take the clean sensor level data , do the projection 
to source level, perform time-frequency analysis there and then based on 
the complex spectral coefficients compute cross-frequency coupling.


Let me know if I can help more

Best

Giorgos





On 2/9/2017 12:16 AM, Ajilore, Olusola wrote:


Hello,

The current HCP MEG source-level data includes within frequency band 
power envelope correlations. I wanted to calculate cross-frequency 
correlations with the same dataset. Can this be done with source-level 
data (*.ptseries.nii) or does it have done at an earlier stage in the 
pipeline?


Thank you,

Olu Ajilore, MD,PhD

Associate Professor

Associate Director, Residency Training and Education

Co-Director, Adult/Neuroscience Research Track

Department of Psychiatry

University of Illinois-Chicago

oajil...@psych.uic.edu 

brain.uic.edu 

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