If you use Connectome Workbench or FSLView with the labels on, these will indicate which is left and which is right.
Peace, Matt. From: Thomas Arnold <[email protected]<mailto:[email protected]>> Date: Wednesday, October 26, 2016 at 3:26 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] HCP-Users Digest, Vol 47, Issue 32 Hey Matt, Do you know if the NIFTI images have been mirrored or are they in standard left right convention? The average bold values for several right hemisphere regions are greater in the LR runs than in RL runs, however looking at the images mirrored I would have expected the opposite. I've had difficulty finding any reference in the HCP documentation as to which hemisphere signal dropout is lateralized to for the RL and LR cases and thus haven't been able to resolve this. Thank you for your time, Thomas Campbell Arnold On Tue, Oct 25, 2016 at 6:25 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: I recommend taking a look at the SBRef volume included in the downloads to get a sense of that, as I don’t remember off the top of my head. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Arnold, Thomas" <[email protected]<mailto:[email protected]>> Date: Tuesday, October 25, 2016 at 10:44 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] HCP-Users Digest, Vol 47, Issue 32 Which phase encoding method has higher signal dropout in the right hemisphere orbitofrontal cortex, LR or RL? Thomas Arnold ________________________________ From:[email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> on behalf of [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> Sent: Monday, October 24, 2016 6:55:40 PM To: [email protected]<mailto:[email protected]> Subject: HCP-Users Digest, Vol 47, Issue 32 Send HCP-Users mailing list submissions to [email protected]<mailto:[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]<mailto:[email protected]> You can reach the person managing the list at [email protected]<mailto:[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. Re: clamping T1/T2 values in CreateMyelinMaps script of post freesurfer pipeline (Glasser, Matthew) 2. Re: Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii (Gopalakrishnan, Karthik) 3. eLORETA for source reconstruction (mehdy dousty) 4. Re: Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii (Timothy Coalson) 5. Re: Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii (Gopalakrishnan, Karthik) 6. Re: Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii (Timothy Coalson) 7. Re: eLORETA for source reconstruction (Georgios Michalareas) 8. Re: eLORETA for source reconstruction (mehdy dousty) 9. Re: eLORETA for source reconstruction (Georgios Michalareas) 10. Re: eLORETA for source reconstruction (Georgios Michalareas) ---------------------------------------------------------------------- Message: 1 Date: Mon, 24 Oct 2016 17:21:04 +0000 From: "Glasser, Matthew" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] clamping T1/T2 values in CreateMyelinMaps script of post freesurfer pipeline To: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <d433ad0f.12afba%[email protected]<mailto:d433ad0f.12afba%[email protected]>> Content-Type: text/plain; charset="us-ascii" You might want to rescale your data so that the ratio values are reasonably close to 1. Peace, Matt. From: <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>> on behalf of "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>> Date: Monday, October 24, 2016 at 10:46 AM To: "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>> Subject: [HCP-Users] clamping T1/T2 values in CreateMyelinMaps script of post freesurfer pipeline Dear HCP guys, Why T1/T2 values are clamped between 0 and 100 (while the T1/T2 values are not bigger than 10) in CreateMyelinMaps script in post freesurfer pipeline (wb-command -volume-math "clamp((T1w / T2w), 0, 100)")? My dataset has a very different range of values, should I stay with the low and high values of 0 and 100 for that command? Or if I change those values, what subsequent changes I need to make for the rest? thanks, Zahra _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]><mailto:[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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20161024/9a76ee16/attachment-0001.html ------------------------------ Message: 2 Date: Mon, 24 Oct 2016 20:33:23 +0000 From: "Gopalakrishnan, Karthik" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii To: "Glasser, Matthew" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <dm5pr07mb2844afe31dae5af241a7fb88bd...@dm5pr07mb2844.namprd07.prod.outlook.com<mailto:dm5pr07mb2844afe31dae5af241a7fb88bd...@dm5pr07mb2844.namprd07.prod.outlook.com>> Content-Type: text/plain; charset="us-ascii" Thanks Matt! So after using wb_command -cifti-separate on the .dlabel.nii file containing the MMP-1.0 parcellation for the hemisphere, we have a .label.gii file representing the 180 ROIs in the corresponding hemisphere. Can someone point out how we could go from this .label.gii file to 180 separate .gii files representing each ROI so that we can run probtrackx with these ROIs for a given subject? We want to be able to run probtrackx using each of the 180 ROIs as seeds to all 180 possible targets. Thanks, Karthik From: Glasser, Matthew [mailto:[email protected]] Sent: Friday, October 21, 2016 4:14 PM To: Gopalakrishnan, Karthik <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii You can convert the CIFTI file to a GIFTI label file using wb_command -cifti-separate. As for going from GIFTI label to surf+label (probtrackx's interpretation of GIFTI), you'll need to use the label2surf. Hopefully either one of the oxford folks can explain how to use that here or on the FSL list. Peace, Matt. From: <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>> on behalf of "Gopalakrishnan, Karthik" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>> Date: Friday, October 21, 2016 at 2:12 PM To: "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>> Subject: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii Hi all, How do we convert a dlabel.nii file containing 180 ROIs (Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii) to a surf.gii file? We want to do that such that the output ROIs can be used in probtracx. Thanks! Regards, Karthik _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]><mailto:[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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20161024/b83e064c/attachment-0001.html ------------------------------ Message: 3 Date: Mon, 24 Oct 2016 20:42:57 +0000 From: mehdy dousty <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] eLORETA for source reconstruction To: [email protected]<mailto:[email protected]> Message-ID: <cacmbph5tty_exf_ir1phl6fjltgqs73fgpwxyqraz5zo8nw...@mail.gmail.com<mailto:cacmbph5tty_exf_ir1phl6fjltgqs73fgpwxyqraz5zo8nw...@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" Hello, I am using HCP MEG resting state to compute source localization. As it is resting state signal and I am using Fieldtirp I have no idea how to compute the noise covariance matrix. Mostly this matrix is computed with ft_timelockanalysis with the window of [-inf 0] in task-based MEG I really appreciate if anybody can help me. Thanks Mehdy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20161024/797a0d3c/attachment-0001.html ------------------------------ Message: 4 Date: Mon, 24 Oct 2016 15:48:57 -0500 From: Timothy Coalson <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii To: "Gopalakrishnan, Karthik" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <CAK_=tawbrOXjE5rp7_3Hu5acaD0Bj+kKxmn=kg5ofey35dv...@mail.gmail.com<mailto:CAK_=tawbrOXjE5rp7_3Hu5acaD0Bj+kKxmn=kg5ofey35dv...@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" http://www.humanconnectome.org/software/workbench-command.php?function=-gifti-all-labels-to-rois http://www.humanconnectome.org/software/workbench-command.php?function=-metric-merge You'll need to run -metric-merge once for each roi to get them all as separate files, wb_command doesn't generate hundreds of files from a simple command. Tim On Mon, Oct 24, 2016 at 3:33 PM, Gopalakrishnan, Karthik < [email protected]<mailto:[email protected]>> wrote: > Thanks Matt! > > > > So after using wb_command -cifti-separate on the .dlabel.nii file > containing the MMP-1.0 parcellation for the hemisphere, we have a > .label.gii file representing the 180 ROIs in the corresponding hemisphere. > > > > Can someone point out how we could go from this .label.gii file to 180 > separate .gii files representing each ROI so that we can run probtrackx > with these ROIs for a given subject? We want to be able to run probtrackx > using each of the 180 ROIs as seeds to all 180 possible targets. > > > > Thanks, > > Karthik > > > > *From:* Glasser, Matthew [mailto:[email protected]] > *Sent:* Friday, October 21, 2016 4:14 PM > *To:* Gopalakrishnan, Karthik > <[email protected]<mailto:[email protected]>>; > [email protected]<mailto:[email protected]> > *Subject:* Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to > surf.gii > > > > You can convert the CIFTI file to a GIFTI label file using wb_command > -cifti-separate. As for going from GIFTI label to surf+label (probtrackx?s > interpretation of GIFTI), you?ll need to use the label2surf. Hopefully > either one of the oxford folks can explain how to use that here or on the > FSL list. > > > > Peace, > > > > Matt. > > > > *From: > *<[email protected]<mailto:[email protected]>> > on behalf of > "Gopalakrishnan, Karthik" <[email protected]<mailto:[email protected]>> > *Date: *Friday, October 21, 2016 at 2:12 PM > *To: *"[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > *Subject: *[HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to > surf.gii > > > > Hi all, > > > > How do we convert a dlabel.nii file containing 180 ROIs > (Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii) > to a surf.gii file? We want to do that such that the output ROIs can be > used in probtracx. > > > > Thanks! > > > > Regards, > > Karthik > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[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. > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[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/20161024/5aa47a2f/attachment-0001.html ------------------------------ Message: 5 Date: Mon, 24 Oct 2016 21:56:43 +0000 From: "Gopalakrishnan, Karthik" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii To: Timothy Coalson <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <dm5pr07mb28443e807f303f2e91e68871bd...@dm5pr07mb2844.namprd07.prod.outlook.com<mailto:dm5pr07mb28443e807f303f2e91e68871bd...@dm5pr07mb2844.namprd07.prod.outlook.com>> Content-Type: text/plain; charset="utf-8" Thanks Tim! For running with the option -gifti-all-labels-to-rois, we need to provide a <map> as per the documentation in the first link you shared. What do we provide as <map>? We tried passing the number 1 and got a .func.gii file representing the ROI having Key=1 in the input XML. We then thought passing 2, 3, ?, 180 would give us the ROIs having those values as the keys in the input XML but we got an error as follows: ERROR: Invalid map number or name specified Could you share what we should provide as <map>? We printed the input XML and saw that the map name was #1 and then tried passing that, but that gave us some error as well. Our understanding of what you?ve said is that we need to create a single metric .func.gii file representing all the 180 ROIs by running using the -gifti-all-labels-to-rois option exactly once (which we couldn?t do as explained above), followed by running -metric-merge 180 times, each time passing -column as the values in the integer set [1, 180]. Is this right? Thanks! Karthik From: Timothy Coalson [mailto:[email protected]] Sent: Monday, October 24, 2016 4:49 PM To: Gopalakrishnan, Karthik <[email protected]<mailto:[email protected]>> Cc: Glasser, Matthew <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii http://www.humanconnectome.org/software/workbench-command.php?function=-gifti-all-labels-to-rois http://www.humanconnectome.org/software/workbench-command.php?function=-metric-merge You'll need to run -metric-merge once for each roi to get them all as separate files, wb_command doesn't generate hundreds of files from a simple command. Tim On Mon, Oct 24, 2016 at 3:33 PM, Gopalakrishnan, Karthik <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>> wrote: Thanks Matt! So after using wb_command -cifti-separate on the .dlabel.nii file containing the MMP-1.0 parcellation for the hemisphere, we have a .label.gii file representing the 180 ROIs in the corresponding hemisphere. Can someone point out how we could go from this .label.gii file to 180 separate .gii files representing each ROI so that we can run probtrackx with these ROIs for a given subject? We want to be able to run probtrackx using each of the 180 ROIs as seeds to all 180 possible targets. Thanks, Karthik From: Glasser, Matthew [mailto:[email protected]<mailto:[email protected]<mailto:[email protected]%3Cmailto:[email protected]>>] Sent: Friday, October 21, 2016 4:14 PM To: Gopalakrishnan, Karthik <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>>; [email protected]<mailto:[email protected]><mailto:[email protected]> Subject: Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii You can convert the CIFTI file to a GIFTI label file using wb_command -cifti-separate. As for going from GIFTI label to surf+label (probtrackx?s interpretation of GIFTI), you?ll need to use the label2surf. Hopefully either one of the oxford folks can explain how to use that here or on the FSL list. Peace, Matt. From: <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>> on behalf of "Gopalakrishnan, Karthik" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>> Date: Friday, October 21, 2016 at 2:12 PM To: "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]%3E>> Subject: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii Hi all, How do we convert a dlabel.nii file containing 180 ROIs (Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii) to a surf.gii file? We want to do that such that the output ROIs can be used in probtracx. Thanks! Regards, Karthik _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]><mailto:[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. _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]><mailto:[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/20161024/5404bde2/attachment-0001.html ------------------------------ Message: 6 Date: Mon, 24 Oct 2016 17:31:45 -0500 From: Timothy Coalson <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii To: "Gopalakrishnan, Karthik" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <CAK_=tay2t1MMgeupThgBK83MHfhf=vpsc52jchajn4asbcv...@mail.gmail.com<mailto:CAK_=tay2t1MMgeupThgBK83MHfhf=vpsc52jchajn4asbcv...@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" 1 is correct for <map>, take another look at the output file, and note that it has 180 columns in it. Yes, that is what I meant about -metric-merge. Tim On Mon, Oct 24, 2016 at 4:56 PM, Gopalakrishnan, Karthik < [email protected]<mailto:[email protected]>> wrote: > Thanks Tim! > > > > For running with the option -gifti-all-labels-to-rois, we need to provide > a <map> as per the documentation in the first link you shared. What do we > provide as <map>? We tried passing the number 1 and got a .func.gii file > representing the ROI having Key=1 in the input XML. We then thought passing > 2, 3, ?, 180 would give us the ROIs having those values as the keys in the > input XML but we got an error as follows: > > > > ERROR: Invalid map number or name specified > > > > Could you share what we should provide as <map>? We printed the input XML > and saw that the map name was #1 and then tried passing that, but that gave > us some error as well. > > > > Our understanding of what you?ve said is that we need to create a single > metric .func.gii file representing all the 180 ROIs by running using the > -gifti-all-labels-to-rois option exactly once (which we couldn?t do as > explained above), followed by running -metric-merge 180 times, each time > passing -column as the values in the integer set [1, 180]. Is this right? > > > > Thanks! > > Karthik > > > > *From:* Timothy Coalson [mailto:[email protected]] > *Sent:* Monday, October 24, 2016 4:49 PM > *To:* Gopalakrishnan, Karthik > <[email protected]<mailto:[email protected]>> > *Cc:* Glasser, Matthew <[email protected]<mailto:[email protected]>>; > [email protected]<mailto:[email protected]> > > *Subject:* Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to > surf.gii > > > > http://www.humanconnectome.org/software/workbench- > command.php?function=-gifti-all-labels-to-rois > > > > http://www.humanconnectome.org/software/workbench- > command.php?function=-metric-merge > > > > You'll need to run -metric-merge once for each roi to get them all as > separate files, wb_command doesn't generate hundreds of files from a simple > command. > > > > Tim > > > > > > On Mon, Oct 24, 2016 at 3:33 PM, Gopalakrishnan, Karthik < > [email protected]<mailto:[email protected]>> wrote: > > Thanks Matt! > > > > So after using wb_command -cifti-separate on the .dlabel.nii file > containing the MMP-1.0 parcellation for the hemisphere, we have a > .label.gii file representing the 180 ROIs in the corresponding hemisphere. > > > > Can someone point out how we could go from this .label.gii file to 180 > separate .gii files representing each ROI so that we can run probtrackx > with these ROIs for a given subject? We want to be able to run probtrackx > using each of the 180 ROIs as seeds to all 180 possible targets. > > > > Thanks, > > Karthik > > > > *From:* Glasser, Matthew [mailto:[email protected]] > *Sent:* Friday, October 21, 2016 4:14 PM > *To:* Gopalakrishnan, Karthik > <[email protected]<mailto:[email protected]>>; > [email protected]<mailto:[email protected]> > *Subject:* Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to > surf.gii > > > > You can convert the CIFTI file to a GIFTI label file using wb_command > -cifti-separate. As for going from GIFTI label to surf+label (probtrackx?s > interpretation of GIFTI), you?ll need to use the label2surf. Hopefully > either one of the oxford folks can explain how to use that here or on the > FSL list. > > > > Peace, > > > > Matt. > > > > *From: > *<[email protected]<mailto:[email protected]>> > on behalf of > "Gopalakrishnan, Karthik" <[email protected]<mailto:[email protected]>> > *Date: *Friday, October 21, 2016 at 2:12 PM > *To: *"[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > *Subject: *[HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to > surf.gii > > > > Hi all, > > > > How do we convert a dlabel.nii file containing 180 ROIs > (Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii) > to a surf.gii file? We want to do that such that the output ROIs can be > used in probtracx. > > > > Thanks! > > > > Regards, > > Karthik > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[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. > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[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/20161024/a1157690/attachment-0001.html ------------------------------ Message: 7 Date: Tue, 25 Oct 2016 00:40:23 +0200 From: Georgios Michalareas <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] eLORETA for source reconstruction To: <[email protected]<mailto:[email protected]>> Message-ID: <[email protected]<mailto:[email protected]>> Content-Type: text/plain; charset="utf-8"; format=flowed Hi , I think you can still do it with ft_timelockanalysis. I assume that the resting state data you mention has only one trial. then if you just do: cfg=[]; cfg.covariance='yes'; pseudoavg=ft_timelockanalysis(cfg, data); then it will just compute the average across trials but as there is only one trial it will basically produce the exact same data. But in the output of timelockanalysis you ll find a field .cov whith dimension Nchannels x Nchannels which contains the covariance matrix of the MEG sensors . This covariance has been computed from the entire length of the single resting state trial , so I think this is what you are interested in. I hope this helps. Best Giorgos On 10/24/2016 10:42 PM, mehdy dousty wrote: > Hello, > I am using HCP MEG resting state to compute source localization. As it > is resting state signal and I am using Fieldtirp I have no idea how to > compute the noise covariance matrix. Mostly this matrix is computed > with ft_timelockanalysis with the window of [-inf 0] in task-based MEG > I really appreciate if anybody can help me. > Thanks > Mehdy > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ------------------------------ Message: 8 Date: Mon, 24 Oct 2016 22:56:30 +0000 From: mehdy dousty <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] eLORETA for source reconstruction To: Georgios Michalareas <[email protected]<mailto:[email protected]>>, [email protected]<mailto:[email protected]> Message-ID: <cacmbph4t-wi0ehns-494y85cosxs_f+ehpq-maupcrt6ows...@mail.gmail.com<mailto:cacmbph4t-wi0ehns-494y85cosxs_f+ehpq-maupcrt6ows...@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" Thanks for your answer. as it is resting state I can have 1 trial or keep the trial existed in the pre-processed signals,147trails, Based on the paper by Sylvain Baillet with title of "The brain resting-state activity is shaped by synchronized cross-frequency coupling of neural oscillations" the covariance matrix is empirically estimated by empty-room recording, therefore as the room noise and participant noise is provided by HCP I don't know which level of noise do I need to take, or I don't need to consider that and just simply did what you have proposed. Thanks On Mon, Oct 24, 2016 at 4:40 PM Georgios Michalareas < [email protected]<mailto:[email protected]>> wrote: > Hi , > > I think you can still do it with ft_timelockanalysis. > > I assume that the resting state data you mention has only one trial. > > then if you just do: > > cfg=[]; > > cfg.covariance='yes'; > > pseudoavg=ft_timelockanalysis(cfg, data); > > > then it will just compute the average across trials but as there is only > one trial it will basically produce the exact same data. > > But in the output of timelockanalysis you ll find a field .cov whith > dimension Nchannels x Nchannels which contains the covariance matrix of > the MEG sensors . > > This covariance has been computed from the entire length of the single > resting state trial , so I think this is what you are interested in. > > I hope this helps. > > Best > > Giorgos > > > On 10/24/2016 10:42 PM, mehdy dousty wrote: > > Hello, > > I am using HCP MEG resting state to compute source localization. As it > > is resting state signal and I am using Fieldtirp I have no idea how to > > compute the noise covariance matrix. Mostly this matrix is computed > > with ft_timelockanalysis with the window of [-inf 0] in task-based MEG > > I really appreciate if anybody can help me. > > Thanks > > Mehdy > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected]<mailto:[email protected]> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[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/20161024/99daadf9/attachment-0001.html ------------------------------ Message: 9 Date: Tue, 25 Oct 2016 00:57:36 +0200 From: Georgios Michalareas <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] eLORETA for source reconstruction To: <[email protected]<mailto:[email protected]>> Message-ID: <[email protected]<mailto:[email protected]>> Content-Type: text/plain; charset="utf-8"; format=flowed Hi again, I think I misunderstood your question before. I think by noise you mean a baseline compared to which you compare your actual activity. Well the problem with resting state is that there is no baseline and doing a singular value decomposition and taking the smaller eigenvalue of the covariance matrix is not going to take you far. I think your best bet is to use the empty room scans that are given in the HCP. These are empty room scans just before the resting state sessions so you can use these as baseline. I hope this helps this time Best Giorgos On 10/24/2016 10:42 PM, mehdy dousty wrote: > Hello, > I am using HCP MEG resting state to compute source localization. As it > is resting state signal and I am using Fieldtirp I have no idea how to > compute the noise covariance matrix. Mostly this matrix is computed > with ft_timelockanalysis with the window of [-inf 0] in task-based MEG > I really appreciate if anybody can help me. > Thanks > Mehdy > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ------------------------------ Message: 10 Date: Tue, 25 Oct 2016 01:01:33 +0200 From: Georgios Michalareas <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] eLORETA for source reconstruction To: mehdy dousty <[email protected]<mailto:[email protected]>>, <[email protected]<mailto:[email protected]>> Message-ID: <[email protected]<mailto:[email protected]>> Content-Type: text/plain; charset="utf-8" I recommend that you should start with the empty room noise rather than the participant noise. Giorgos On 10/25/2016 12:56 AM, mehdy dousty wrote: > Thanks for your answer. as it is resting state I can have 1 trial or > keep the trial existed in the pre-processed signals,147trails, Based > on the paper by Sylvain Baillet with title of "The brain resting-state > activity is shaped by synchronized cross-frequency coupling of neural > oscillations" the covariance matrix is empirically estimated by > empty-room recording, therefore as the room noise and participant > noise is provided by HCP I don't know which level of noise do I need > to take, or I don't need to consider that and just simply did what you > have proposed. > Thanks > > On Mon, Oct 24, 2016 at 4:40 PM Georgios Michalareas > <[email protected]<mailto:[email protected]> > <mailto:[email protected]>> wrote: > > Hi , > > I think you can still do it with ft_timelockanalysis. > > I assume that the resting state data you mention has only one trial. > > then if you just do: > > cfg=[]; > > cfg.covariance='yes'; > > pseudoavg=ft_timelockanalysis(cfg, data); > > > then it will just compute the average across trials but as there > is only > one trial it will basically produce the exact same data. > > But in the output of timelockanalysis you ll find a field .cov whith > dimension Nchannels x Nchannels which contains the covariance > matrix of > the MEG sensors . > > This covariance has been computed from the entire length of the single > resting state trial , so I think this is what you are interested in. > > I hope this helps. > > Best > > Giorgos > > > On 10/24/2016 10:42 PM, mehdy dousty wrote: > > Hello, > > I am using HCP MEG resting state to compute source localization. > As it > > is resting state signal and I am using Fieldtirp I have no idea > how to > > compute the noise covariance matrix. Mostly this matrix is computed > > with ft_timelockanalysis with the window of [-inf 0] in > task-based MEG > > I really appreciate if anybody can help me. > > Thanks > > Mehdy > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected]<mailto:[email protected]> > <mailto:[email protected]> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > <mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > -------------- next part -------------- An HTML attachment was scrubbed... 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