seed to seed resting state?

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Corinna Bauer

2 Mar 2017 2 Mar '17

12:09 p.m.

Hi all,

I was just wondering if it was possible to do seed to seed resting state analysis in freesurfer, rather than seed to voxel? I am wanting to examine connectivity within specific Yeo networks, using a spherical ROI as a seed. The spherical ROI will be generated from one of the peak areas of activation listed in the original 7 network Yeo paper.

Thanks

Corinna

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Corinna Bauer

6 Mar 6 Mar

9:52 a.m.

Hi, just following up on this question to see if there were any suggestions for how to best complete seed to seed RS analysis in FreeSurfer.

Thanks!

Corinna

On Thu, Mar 2, 2017 at 12:09 PM, Corinna Bauer corinnab83@gmail.com wrote:

...

Hi all,

I was just wondering if it was possible to do seed to seed resting state analysis in freesurfer, rather than seed to voxel? I am wanting to examine connectivity within specific Yeo networks, using a spherical ROI as a seed. The spherical ROI will be generated from one of the peak areas of activation listed in the original 7 network Yeo paper.

Thanks

Corinna

Douglas N Greve

1:13 p.m.

Try fcseedcor. Run with -help to get docs

On 03/06/2017 09:52 AM, Corinna Bauer wrote:

...

Hi, just following up on this question to see if there were any suggestions for how to best complete seed to seed RS analysis in FreeSurfer.

Thanks!

Corinna

On Thu, Mar 2, 2017 at 12:09 PM, Corinna Bauer <corinnab83@gmail.com mailto:corinnab83@gmail.com> wrote:
Hi all,

I was just wondering if it was possible to do seed to seed resting
state analysis in freesurfer, rather than seed to voxel? I am
wanting to examine connectivity within specific Yeo networks,
using a spherical ROI as a seed. The spherical ROI will be
generated from one of the peak areas of activation listed in the
original 7 network Yeo paper.

Thanks

Corinna
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Jinsong Tang

7 Mar 7 Mar

8:18 p.m.

Hi Doug，

I am also interested in seed to seed resting state analysis.

It seems no fcseedcor command in Freesurfer v5.3.? Is it command in v6.0?

Thanks and best,

Jinsong

On Mon, Mar 6, 2017 at 10:13 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

Try fcseedcor. Run with -help to get docs

On 03/06/2017 09:52 AM, Corinna Bauer wrote:

...
Hi, just following up on this question to see if there were any suggestions for how to best complete seed to seed RS analysis in FreeSurfer.

Thanks!

Corinna

On Thu, Mar 2, 2017 at 12:09 PM, Corinna Bauer <corinnab83@gmail.com mailto:corinnab83@gmail.com> wrote:
Hi all,

I was just wondering if it was possible to do seed to seed resting
state analysis in freesurfer, rather than seed to voxel? I am
wanting to examine connectivity within specific Yeo networks,
using a spherical ROI as a seed. The spherical ROI will be
generated from one of the peak areas of activation listed in the
original 7 network Yeo paper.

Thanks

Corinna
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

-- Jinsong Tang, MD Institute of Mental Health The Second Xiangya Hospital , Central South University 139 Renmin Road, Changsha Hunan 410011, P.R. China

Douglas Greve

9:36 p.m.

yes, v6

On 3/7/17 8:18 PM, Jinsong Tang wrote:

...

Hi Doug，

I am also interested in seed to seed resting state analysis.

It seems no fcseedcor command in Freesurfer v5.3.? Is it command in v6.0?

Thanks and best,

Jinsong

On Mon, Mar 6, 2017 at 10:13 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Try fcseedcor. Run with -help to get docs


On 03/06/2017 09:52 AM, Corinna Bauer wrote:
> Hi, just following up on this question to see if there were any
> suggestions for how to best complete seed to seed RS analysis in
> FreeSurfer.
>
> Thanks!
>
> Corinna
>
> On Thu, Mar 2, 2017 at 12:09 PM, Corinna Bauer
<corinnab83@gmail.com <mailto:corinnab83@gmail.com>
> <mailto:corinnab83@gmail.com <mailto:corinnab83@gmail.com>>> wrote:
>
>     Hi all,
>
>     I was just wondering if it was possible to do seed to seed
resting
>     state analysis in freesurfer, rather than seed to voxel? I am
>     wanting to examine connectivity within specific Yeo networks,
>     using a spherical ROI as a seed. The spherical ROI will be
>     generated from one of the peak areas of activation listed in the
>     original 7 network Yeo paper.
>
>     Thanks
>
>     Corinna
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline
<http://www.partners.org/complianceline> . If the e-mail was sent
to you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

-- Jinsong Tang, MD Institute of Mental Health The Second Xiangya Hospital , Central South University 139 Renmin Road, Changsha Hunan 410011, P.R. China

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Corinna Bauer

29 Mar 29 Mar

10:21 a.m.

Is there a way to implement it in an earlier version?

On Tue, Mar 7, 2017 at 9:36 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:

...

yes, v6

On 3/7/17 8:18 PM, Jinsong Tang wrote:

Hi Doug，

I am also interested in seed to seed resting state analysis.

It seems no fcseedcor command in Freesurfer v5.3.? Is it command in v6.0?

Thanks and best,

Jinsong

On Mon, Mar 6, 2017 at 10:13 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:

...
Try fcseedcor. Run with -help to get docs

On 03/06/2017 09:52 AM, Corinna Bauer wrote:

...
Hi, just following up on this question to see if there were any suggestions for how to best complete seed to seed RS analysis in FreeSurfer.

Thanks!

Corinna

On Thu, Mar 2, 2017 at 12:09 PM, Corinna Bauer <corinnab83@gmail.com mailto:corinnab83@gmail.com> wrote:
Hi all,

I was just wondering if it was possible to do seed to seed resting
state analysis in freesurfer, rather than seed to voxel? I am
wanting to examine connectivity within specific Yeo networks,
using a spherical ROI as a seed. The spherical ROI will be
generated from one of the peak areas of activation listed in the
original 7 network Yeo paper.

Thanks

Corinna
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 <(617)%20724-2358> Fax: 617-726-7422 <(617)%20726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Jinsong Tang, MD Institute of Mental Health The Second Xiangya Hospital , Central South University 139 Renmin Road, Changsha Hunan 410011, P.R. China

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Douglas N Greve

12:10 p.m.

No, but I think you can just use fcseedcor in v5.3.

On 03/29/2017 10:21 AM, Corinna Bauer wrote:

...

Is there a way to implement it in an earlier version?

On Tue, Mar 7, 2017 at 9:36 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

yes, v6


On 3/7/17 8:18 PM, Jinsong Tang wrote:

...

Hi  Doug，

I am also interested in seed to seed resting state analysis.

It seems no fcseedcor command in Freesurfer v5.3.?  Is it command
in v6.0?

Thanks and best,

Jinsong




On Mon, Mar 6, 2017 at 10:13 AM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    Try fcseedcor. Run with -help to get docs


    On 03/06/2017 09:52 AM, Corinna Bauer wrote:
    > Hi, just following up on this question to see if there were any
    > suggestions for how to best complete seed to seed RS
    analysis in
    > FreeSurfer.
    >
    > Thanks!
    >
    > Corinna
    >
    > On Thu, Mar 2, 2017 at 12:09 PM, Corinna Bauer
    <corinnab83@gmail.com <mailto:corinnab83@gmail.com>
    > <mailto:corinnab83@gmail.com
    <mailto:corinnab83@gmail.com>>> wrote:
    >
    >     Hi all,
    >
    >     I was just wondering if it was possible to do seed to
    seed resting
    >     state analysis in freesurfer, rather than seed to
    voxel? I am
    >     wanting to examine connectivity within specific Yeo
    networks,
    >     using a spherical ROI as a seed. The spherical ROI will be
    >     generated from one of the peak areas of activation
    listed in the
    >     original 7 network Yeo paper.
    >
    >     Thanks
    >
    >     Corinna
    >
    >
    >
    >
    > _______________________________________________
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    >
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
    Fax: 617-726-7422 <tel:%28617%29%20726-7422>

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
    <https://gate.nmr.mgh.harvard.edu/filedrop2>
    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    Outgoing:
    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
    <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>

    _______________________________________________
    Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>


    The information in this e-mail is intended only for the
    person to whom it is
    addressed. If you believe this e-mail was sent to you in
    error and the e-mail
    contains patient information, please contact the Partners
    Compliance HelpLine at
    http://www.partners.org/complianceline
    <http://www.partners.org/complianceline> . If the e-mail was
    sent to you in error
    but does not contain patient information, please contact the
    sender and properly
    dispose of the e-mail.




-- 
Jinsong Tang, MD
Institute of Mental Health
The Second Xiangya Hospital , Central South University
139 Renmin Road, Changsha Hunan 410011, P.R. China


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

_______________________________________________ Freesurfer mailing
list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The
information in this e-mail is intended only for the person to whom
it is addressed. If you believe this e-mail was sent to you in
error and the e-mail contains patient information, please contact
the Partners Compliance HelpLine at
http://www.partners.org/complianceline
<http://www.partners.org/complianceline> . If the e-mail was sent
to you in error but does not contain patient information, please
contact the sender and properly dispose of the e-mail.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Corinna Bauer
Douglas Greve
Douglas N Greve
Jinsong Tang