Thanks Doug,
I used the command "mris_calc gammavar.mgh sqrt" and the output was: "Saving result to 'out.mgz' (type = MGH )"
Then I ran the command "mris_calc out.mgz stats" and the output was :
Size [ 163842 ]
Min@(index) [ 0.000000 (161385) ]
Max@(index) [ 0.259395 (18208) ]
Mean [ 0.097956 ]
Std [ 0.040943 ]
Sum [ 16049.365234 ]
Prod [ 0.000000 ]
Min@(index) [ 0.000000 (161385) ]
Max@(index) [ 0.259395 (18208) ]
Mean [ 0.097956 ]
Std [ 0.040943 ]
Sum [ 16049.365234 ]
Prod [ 0.000000 ]
In order to calculate the standard error is it fine if I use mris_calc gammavar.mgh stats the I divide the Std of gammavar.mgh by the square root of the sample size ( number of subjects included in the analysis)?
Thanks a lot!
Sent: Monday, December 21, 2015 at 2:44 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec visualization
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec visualization
it helps to see the error msg, but my guess is that you need to specify
an mgh file, not a txt file. This will give you the voxel-wise stderr,
not a standard error for the cluster (which does not make sense)
On 12/21/2015 02:38 PM, John Anderson wrote:
> Hi Doug,
> Given that the standard variance can be calculated using the command
> "mris_calc" and the flag "-sqrt" what is the correct command to do
> this calculation?
> I tried:
> mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly
> what I am doing wrong?
> Bests,
> John
> *Sent:* Monday, December 21, 2015 at 2:20 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec visualization
> QDEC cannot but the information may be in the output folder. There
> should be a file called gammavar.mgh. This will be the standard variance
> (so take the square root)
>
> On 12/21/2015 02:08 PM, John Anderson wrote:
> > Thanks you very much Doug,
> > Please one more question. Is there any way in Qdec to get the stamdard
> > error (SE) ?
> > Bests,
> > John
> > *Sent:* Monday, December 21, 2015 at 11:43 AM
> > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] Qdec visualization
> > The correction for multiple comparisons is cluster-based. Each cluster
> > gets a single number. In the display, all the vertices get that same
> > number.
> >
> > On 12/18/2015 03:17 PM, John Anderson wrote:
> > > Hi Freesurfer experts,
> > > I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> > > comparisons between two groups.
> > >
> > > Before corrcting the results for multiple comparisons ( monte carlo
> > > simulation) the significant differnce between the groups is visualized
> > > as a range of color while after correcting for multiple copmparisons
> > > the color of the statistical map is usinform ( Attached)
> > > Is ther any way to visualze the results as a range of color after
> > > correcting the results for multiple comparsiosn
> > >
> > > Thanks in advance for any advice
> > > Bests,
> > > John Anderson
> > >
> > > Senior Research Associate
> > > Psychological and Brain Sciences Dept.
> > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > > Phone: +1 (603) 646-9834
> > > Fax: +1 (603) 646-1419
> > >
> > >
> > > _______________________________________________
> > > 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>
> > <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
> <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
>
>
> _______________________________________________
> 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
an mgh file, not a txt file. This will give you the voxel-wise stderr,
not a standard error for the cluster (which does not make sense)
On 12/21/2015 02:38 PM, John Anderson wrote:
> Hi Doug,
> Given that the standard variance can be calculated using the command
> "mris_calc" and the flag "-sqrt" what is the correct command to do
> this calculation?
> I tried:
> mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly
> what I am doing wrong?
> Bests,
> John
> *Sent:* Monday, December 21, 2015 at 2:20 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec visualization
> QDEC cannot but the information may be in the output folder. There
> should be a file called gammavar.mgh. This will be the standard variance
> (so take the square root)
>
> On 12/21/2015 02:08 PM, John Anderson wrote:
> > Thanks you very much Doug,
> > Please one more question. Is there any way in Qdec to get the stamdard
> > error (SE) ?
> > Bests,
> > John
> > *Sent:* Monday, December 21, 2015 at 11:43 AM
> > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] Qdec visualization
> > The correction for multiple comparisons is cluster-based. Each cluster
> > gets a single number. In the display, all the vertices get that same
> > number.
> >
> > On 12/18/2015 03:17 PM, John Anderson wrote:
> > > Hi Freesurfer experts,
> > > I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> > > comparisons between two groups.
> > >
> > > Before corrcting the results for multiple comparisons ( monte carlo
> > > simulation) the significant differnce between the groups is visualized
> > > as a range of color while after correcting for multiple copmparisons
> > > the color of the statistical map is usinform ( Attached)
> > > Is ther any way to visualze the results as a range of color after
> > > correcting the results for multiple comparsiosn
> > >
> > > Thanks in advance for any advice
> > > Bests,
> > > John Anderson
> > >
> > > Senior Research Associate
> > > Psychological and Brain Sciences Dept.
> > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > > Phone: +1 (603) 646-9834
> > > Fax: +1 (603) 646-1419
> > >
> > >
> > > _______________________________________________
> > > 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>
> > <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
> <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
>
>
> _______________________________________________
> 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.
