subject:"Re\: \[HCP\-Users\] Resting state networks"

Re: [HCP-Users] Resting state networks

2019-03-25 Thread Glasser, Matthew

Right.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Claude Bajada 
mailto:c.baj...@fz-juelich.de>>
Date: Monday, March 25, 2019 at 5:39 AM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Resting state networks

Thanks for your reply Tim, by "least pairing an LR with an RL" I assume you 
mean concatenate the time series, correct?

Claude

On 22/03/2019 19:19, Timothy Coalson wrote:
Inline replies.

Tim

On Fri, Mar 22, 2019 at 10:17 AM Claude Bajada 
mailto:c.baj...@fz-juelich.de>> wrote:
Dear experts,

Could I just confirm that the data that is found in:

${SubjectFolder}/MNINinLinear/Results/rfMRI_REST?_LR/rfMRI_REST?_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii

Is the resting state data using the MSMall aligned vertex coordinates

Yes.

and that these data can be used to then produce Resting state networks

Yes.

(I realize that these are available but I just want to make sure I am
understanding the data that I have). Further are the four subfolders in
"Results" four separate runs that I can either concatenate or produce
four different RSNs?

Yes, but the LR and RL runs have different locations of signal dropout, so we 
generally recommend at least pairing an LR with an RL to increase the overall 
coverage.

Am I also correct in assuming that these data are not smoothed?

No, there is a small amount of added smoothing done (2mm FWHM) while putting 
the data into ~2mm grayordinates space - this could be done without any added 
smoothing, but for historical reasons we have kept it consistent with earlier 
releases.  Of course, this amount doesn't approach the smoothing done in many 
non-HCP analysis streams.

Regards,

Claude

Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

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Re: [HCP-Users] Resting state networks

2019-03-25 Thread Claude Bajada

Thanks for your reply Tim, by "least pairing an LR with an RL" I assume
you mean concatenate the time series, correct?

Claude

On 22/03/2019 19:19, Timothy Coalson wrote:

Inline replies.

Tim

On Fri, Mar 22, 2019 at 10:17 AM Claude Bajada > wrote:

Dear experts,

Could I just confirm that the data that is found in:

${SubjectFolder}/MNINinLinear/Results/rfMRI_REST?_LR/rfMRI_REST?_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii

Is the resting state data using the MSMall aligned vertex coordinates

Yes.

and that these data can be used to then produce Resting state networks

Yes.

(I realize that these are available but I just want to make sure I am
understanding the data that I have). Further are the four
subfolders in
"Results" four separate runs that I can either concatenate or produce
four different RSNs?

Yes, but the LR and RL runs have different locations of signal
dropout, so we generally recommend at least pairing an LR with an RL
to increase the overall coverage.

Am I also correct in assuming that these data are not smoothed?

No, there is a small amount of added smoothing done (2mm FWHM) while
putting the data into ~2mm grayordinates space - this could be done
without any added smoothing, but for historical reasons we have kept
it consistent with earlier releases. Of course, this amount doesn't
approach the smoothing done in many non-HCP analysis streams.

Regards,

Claude

Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

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Re: [HCP-Users] Resting state networks

2019-03-22 Thread Timothy Coalson

Inline replies.

Tim


On Fri, Mar 22, 2019 at 10:17 AM Claude Bajada 
wrote:

> Dear experts,
>
> Could I just confirm that the data that is found in:
>
>
> ${SubjectFolder}/MNINinLinear/Results/rfMRI_REST?_LR/rfMRI_REST?_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii
>
> Is the resting state data using the MSMall aligned vertex coordinates
>

Yes.


> and that these data can be used to then produce Resting state networks
>

Yes.


> (I realize that these are available but I just want to make sure I am
> understanding the data that I have). Further are the four subfolders in
> "Results" four separate runs that I can either concatenate or produce
> four different RSNs?
>

Yes, but the LR and RL runs have different locations of signal dropout, so
we generally recommend at least pairing an LR with an RL to increase the
overall coverage.


>
> Am I also correct in assuming that these data are not smoothed?
>

No, there is a small amount of added smoothing done (2mm FWHM) while
putting the data into ~2mm grayordinates space - this could be done without
any added smoothing, but for historical reasons we have kept it consistent
with earlier releases.  Of course, this amount doesn't approach the
smoothing done in many non-HCP analysis streams.


> Regards,
>
> Claude
>
>
>
>
> 
>
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
>
> 
>
> 
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] Resting state networks

Re: [HCP-Users] Resting state networks

Re: [HCP-Users] Resting state networks

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