This si Great!!! Thanks Doug. One more question:
What is the correct input in the command mri_surfcluster. Is it the image "sig.mgh" ?
Bests,
John
John
Sent: Thursday, March 03, 2016 at 12:47 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec-statistical map
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec-statistical map
You will have to extract clusters (mri_surfcluster) to create an
annotation, then use mri_segstats with the --annot option and specifying
the y.mgh file as input and the output using something like --avgwf
output.txt (also add --exludeid 0). The output will have a row for each
frame in y.mgh (ie, each subject) and a column for each cluster
On 03/03/2016 12:43 PM, John Anderson wrote:
> Hi Doug,
> How can I use this statistical map ( e.g. as a mask) to calculate the
> mean cortical thickness only in the areas of significant differnce
> between the groups for every subject?
> Bests,
> John
> *Sent:* Thursday, March 03, 2016 at 12:37 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec-statistical map
> not sure what you mean. the statistical map will have a single value,
> not a value for each subject
>
> On 03/03/2016 12:31 PM, John Anderson wrote:
> > Dear FS experts,
> > I am using Qdec to study the differnce in cortical thicnkess between
> > two groups.
> > Qdec is running a GLM analysis. This will output a statistical map
> > (sig.mgh) for the differnce between the groups in cortical thicnkess.
> > How can I extract the numbers of cortical thickness for every
> > subject (depending on the order of subjects in Qdec table) from this
> > statistical map ?
> > Bests,
> > John
> >
> >
> > _______________________________________________
> > 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
> gr...@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
> <http://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.
>
>
> _______________________________________________
> 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
gr...@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
annotation, then use mri_segstats with the --annot option and specifying
the y.mgh file as input and the output using something like --avgwf
output.txt (also add --exludeid 0). The output will have a row for each
frame in y.mgh (ie, each subject) and a column for each cluster
On 03/03/2016 12:43 PM, John Anderson wrote:
> Hi Doug,
> How can I use this statistical map ( e.g. as a mask) to calculate the
> mean cortical thickness only in the areas of significant differnce
> between the groups for every subject?
> Bests,
> John
> *Sent:* Thursday, March 03, 2016 at 12:37 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec-statistical map
> not sure what you mean. the statistical map will have a single value,
> not a value for each subject
>
> On 03/03/2016 12:31 PM, John Anderson wrote:
> > Dear FS experts,
> > I am using Qdec to study the differnce in cortical thicnkess between
> > two groups.
> > Qdec is running a GLM analysis. This will output a statistical map
> > (sig.mgh) for the differnce between the groups in cortical thicnkess.
> > How can I extract the numbers of cortical thickness for every
> > subject (depending on the order of subjects in Qdec table) from this
> > statistical map ?
> > Bests,
> > John
> >
> >
> > _______________________________________________
> > 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
> gr...@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
> <http://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
> 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.
>
>
> _______________________________________________
> 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
gr...@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
_______________________________________________ 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.
