Thanks for your detailed replay. 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 [email protected] brain.uic.edu
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: Thursday, February 09, 2017 12:00 PM To: [email protected] Subject: HCP-Users Digest, Vol 51, Issue 12 Send HCP-Users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://lists.humanconnectome.org/mailman/listinfo/hcp-users or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of HCP-Users digest..." Today's Topics: 1. Calculating cross-frequency power envelope correlations with HCP MEG dataset (Ajilore, Olusola) 2. Re: Calculating cross-frequency power envelope correlations with HCP MEG dataset (Georgios Michalareas) 3. aws cp failed (Kevin LARCHER) 4. Re: Motor task contrats: no RH-cue, LH-cue, etc.? (Burgess, Gregory) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Feb 2017 17:16:50 -0600 From: "Ajilore, Olusola" <[email protected]> Subject: [HCP-Users] Calculating cross-frequency power envelope correlations with HCP MEG dataset To: "'[email protected]'" <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" 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 [email protected]<mailto:[email protected]> brain.uic.edu<http://brain.uic.edu/> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20170208/35139271/attachment-0001.html ------------------------------ Message: 2 Date: Thu, 9 Feb 2017 09:10:53 +0100 From: Georgios Michalareas <[email protected]> Subject: Re: [HCP-Users] Calculating cross-frequency power envelope correlations with HCP MEG dataset To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="windows-1252" 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 > > [email protected] <mailto:[email protected]> > > brain.uic.edu <http://brain.uic.edu/> > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20170209/2554ac56/attachment-0001.html ------------------------------ Message: 3 Date: Thu, 9 Feb 2017 11:10:08 -0500 From: Kevin LARCHER <[email protected]> Subject: [HCP-Users] aws cp failed To: <[email protected]> Message-ID: <CAMqC-Dq_azRZmwVgY-5pHRNc=fjodwdmvocudxnxzpvor-h...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" 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 14:49:37 3386464 100307.ArealDistortion_FS.164k_fs_LR.dscalar.nii 2016-02-08 14:49:37 3096548 100307.ArealDistortion_MSMAll.164k_fs_LR.dscalar.nii 2016-02-08 14:49:38 3386464 100307.ArealDistortion_MSMSulc.164k_fs_LR.dscalar.nii 2016-02-08 14:49:38 3090164 100307.BA.164k_fs_LR.dlabel.nii 2016-02-08 14:49:38 3096548 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 14:49:41 2651457 100307.L.flat.164k_fs_LR.surf.gii 2016-02-08 14:49:42 3635412 100307.L.inflated.164k_fs_LR.surf.gii 2016-02-08 14:49:42 3633563 100307.L.inflated_MSMAll.164k_fs_LR.surf.gii 2016-02-08 14:49:42 3640854 100307.L.midthickness.164k_fs_LR.surf.gii 2016-02-08 14:49:43 3640040 100307.L.midthickness_MSMAll.164k_fs_LR.surf.gii 2016-02-08 14:49:43 3643610 100307.L.pial.164k_fs_LR.surf.gii 2016-02-08 14:49:43 3642908 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 14:49:44 3614784 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 14:49:46 3633792 100307.L.very_inflated.164k_fs_LR.surf.gii 2016-02-08 14:49:46 3631135 100307.L.very_inflated_MSMAll.164k_fs_LR.surf.gii 2016-02-08 14:49:46 3640169 100307.L.white.164k_fs_LR.surf.gii 2016-02-08 14:49:47 3638847 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 14:49:47 3090100 100307.MyelinMap.164k_fs_LR.dscalar.nii 2016-02-08 14:49:48 3090100 100307.MyelinMap_BC.164k_fs_LR.dscalar.nii 2016-02-08 14:49:48 3096388 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 14:49:52 2541434 100307.R.flat.164k_fs_LR.surf.gii 2016-02-08 14:49:53 3510625 100307.R.inflated.164k_fs_LR.surf.gii 2016-02-08 14:49:53 3509516 100307.R.inflated_MSMAll.164k_fs_LR.surf.gii 2016-02-08 14:49:53 3515499 100307.R.midthickness.164k_fs_LR.surf.gii 2016-02-08 14:49:54 3515737 100307.R.midthickness_MSMAll.164k_fs_LR.surf.gii 2016-02-08 14:49:55 3517583 100307.R.pial.164k_fs_LR.surf.gii 2016-02-08 14:49:55 3517793 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 14:49:56 3492005 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 14:49:57 3508069 100307.R.very_inflated.164k_fs_LR.surf.gii 2016-02-08 14:49:57 3506552 100307.R.very_inflated_MSMAll.164k_fs_LR.surf.gii 2016-02-08 14:49:58 3515550 100307.R.white.164k_fs_LR.surf.gii 2016-02-08 14:49:58 3515328 100307.R.white_MSMAll.164k_fs_LR.surf.gii 2016-02-08 14:49:59 3090116 100307.SmoothedMyelinMap.164k_fs_LR.dscalar.nii 2016-02-08 14:49:59 3090132 100307.SmoothedMyelinMap_BC.164k_fs_LR.dscalar.nii 2016-02-08 14:49:59 3096436 100307.SmoothedMyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii 2016-02-08 14:50:00 3096516 100307.SphericalDistortion_MSMAll.164k_fs_LR.dscalar.nii 2016-02-08 14:50:01 3095924 100307.aparc.164k_fs_LR.dlabel.nii 2016-02-08 14:50:01 3106068 100307.aparc.a2009s.164k_fs_LR.dlabel.nii 2016-02-08 14:50:02 3090116 100307.corrThickness.164k_fs_LR.dscalar.nii 2016-02-08 14:50:02 3096356 100307.corrThickness_MSMAll.164k_fs_LR.dscalar.nii 2016-02-08 14:50:02 3090068 100307.curvature.164k_fs_LR.dscalar.nii 2016-02-08 14:50:03 3096308 100307.curvature_MSMAll.164k_fs_LR.dscalar.nii 2016-02-08 14:50:03 3386416 100307.sulc.164k_fs_LR.dscalar.nii 2016-02-08 14:50:04 3096292 100307.sulc_MSMAll.164k_fs_LR.dscalar.nii 2016-02-08 14:50:04 3090100 100307.thickness.164k_fs_LR.dscalar.nii 2016-02-08 14:50:04 3096340 100307.thickness_MSMAll.164k_fs_LR.dscalar.nii 2016-02-08 14:50:05 68348950 BiasField.nii.gz 2016-02-08 19:52:57 75347013 T1w.nii.gz 2016-02-08 21:42:22 3251581 T1w_restore.2.nii.gz 2016-02-08 19:53:02 73773500 T1w_restore.nii.gz 2016-02-08 19:53:07 18806618 T1w_restore_brain.nii.gz 2016-02-08 19:53:09 75487831 T2w.nii.gz 2016-02-08 19:53:14 3261207 T2w_restore.2.nii.gz 2016-02-08 19:53:14 74177645 T2w_restore.nii.gz 2016-02-08 19:53:19 18972749 T2w_restore_brain.nii.gz 2016-02-08 19:53:20 934888 aparc+aseg.nii.gz 2016-02-08 19:53:21 985962 aparc.a2009s+aseg.nii.gz 2016-02-08 19:53:21 321660 brainmask_fs.nii.gz 2016-02-08 19:53:39 718913 ribbon.nii.gz 2016-02-08 19:53:39 1045206 wmparc.nii.gz aws s3 ls s3://hcp-openaccess/HCP_900/100307/MNInonlinear/ (nothing returned at the second try) aws s3 cp s3://hcp-openaccess/HCP_900/100307/MNInonlinear/fsaverage_LR32k . A client error (404) occurred when calling the HeadObject operation: Key "HCP_900/100307/MNInonlinear/fsaverage_LR32k" does not exist Completed 1 part(s) with ... file(s) remaining How can you explain this ? FYI I tried to download from a secured neuroimaging network. Please is there any alternatives to download specific files using aws tools ? -- Regards, Kevin LARCHER, M.Eng. McConnell Brain Imaging Centre Email: [email protected] | [email protected] | [email protected] -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20170209/863bd816/attachment-0001.html ------------------------------ Message: 4 Date: Thu, 9 Feb 2017 16:39:48 +0000 From: "Burgess, Gregory" <[email protected]> Subject: Re: [HCP-Users] Motor task contrats: no RH-cue, LH-cue, etc.? To: Xavier Guell Paradis <[email protected]> Cc: "[email protected]" <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" 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: [email protected] > On Feb 7, 2017, at 12:12 PM, Xavier Guell Paradis <[email protected]> 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 [[email protected]] > Sent: Monday, February 06, 2017 5:18 PM > To: Xavier Guell Paradis > Cc: [email protected] > 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: [email protected] > >> On Feb 3, 2017, at 4:25 PM, Xavier Guell Paradis <[email protected]> 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. >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> 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. ________________________________ 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users End of HCP-Users Digest, Vol 51, Issue 12 ***************************************** _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
