Dear FreeSurfer experts,
I have some questions about corrections for multiple comparisons in FreeSurfer. I have two samples, one consisting of two groups and one consisting of three groups.
I do the comparison with the sample of two groups in qdec. Correcting for multiple comparisons, I get a significant result using FDR, but no significant result using Monte Carlo simulation. How can that be?
I analyze the sample with the three groups by mri_glmfit. In your tutorial, I only found how to correct for multiple comparisons with the Monte Carlo simulation using the command line, but not how to correct with FDR using the command line. Is there a possibility to do this? If not, how many iterations are usual to use within the Monte Carlo simulation?
Any help is appreciated.
Thank you very much,
Marie
they are two different correction schemes. If they gave the same answer, then it would not make sense to have both. the monte carlo tries to compute the probability of a cluster of the given size under the null hypothesis. FDR controls for the number of false positives relative to the total number of positives under the assumption that if any 5% of your positives are false, then you would not change your conclusion.
For monte carlo, we generally use 10000 iterations. If you are using the whole hemisphere, then you can used the cached tables. See the "command-line" tutorial.
doug
On 06/08/2012 08:03 AM, Marie Schneider wrote:
Dear FreeSurfer experts,
I have some questions about corrections for multiple comparisons in FreeSurfer. I have two samples, one consisting of two groups and one consisting of three groups.
I do the comparison with the sample of two groups in qdec. Correcting for multiple comparisons, I get a significant result using FDR, but no significant result using Monte Carlo simulation. How can that be?
I analyze the sample with the three groups by mri_glmfit. In your tutorial, I only found how to correct for multiple comparisons with the Monte Carlo simulation using the command line, but not how to correct with FDR using the command line. Is there a possibility to do this? If not, how many iterations are usual to use within the Monte Carlo simulation?
Any help is appreciated.
Thank you very much,
Marie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you very much for your answer.
Are 10 000 iterations also used when I am running a Monte Carlo simulation in qdec?
Thanks, Marie
2012/6/9 Douglas N Greve greve@nmr.mgh.harvard.edu
they are two different correction schemes. If they gave the same answer, then it would not make sense to have both. the monte carlo tries to compute the probability of a cluster of the given size under the null hypothesis. FDR controls for the number of false positives relative to the total number of positives under the assumption that if any 5% of your positives are false, then you would not change your conclusion.
For monte carlo, we generally use 10000 iterations. If you are using the whole hemisphere, then you can used the cached tables. See the "command-line" tutorial.
doug
On 06/08/2012 08:03 AM, Marie Schneider wrote:
Dear FreeSurfer experts,
I have some questions about corrections for multiple comparisons in FreeSurfer. I have two samples, one consisting of two groups and one consisting of three groups.
I do the comparison with the sample of two groups in qdec. Correcting for multiple comparisons, I get a significant result using FDR, but no significant result using Monte Carlo simulation. How can that be?
I analyze the sample with the three groups by mri_glmfit. In your tutorial, I only found how to correct for multiple comparisons with the Monte Carlo simulation using the command line, but not how to correct with FDR using the command line. Is there a possibility to do this? If not, how many iterations are usual to use within the Monte Carlo simulation?
Any help is appreciated.
Thank you very much,
Marie
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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yes, though I would probably do it outside of qdec as it can take a while (hours or days)
On 06/12/2012 08:03 AM, Marie Schneider wrote:
Thank you very much for your answer.
Are 10 000 iterations also used when I am running a Monte Carlo simulation in qdec?
Thanks, Marie
2012/6/9 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
they are two different correction schemes. If they gave the same answer, then it would not make sense to have both. the monte carlo tries to compute the probability of a cluster of the given size under the null hypothesis. FDR controls for the number of false positives relative to the total number of positives under the assumption that if any 5% of your positives are false, then you would not change your conclusion. For monte carlo, we generally use 10000 iterations. If you are using the whole hemisphere, then you can used the cached tables. See the "command-line" tutorial. doug On 06/08/2012 08:03 AM, Marie Schneider wrote: > Dear FreeSurfer experts, > > I have some questions about corrections for multiple comparisons in > FreeSurfer. I have two samples, one consisting of two groups and one > consisting of three groups. > > I do the comparison with the sample of two groups in qdec. Correcting > for multiple comparisons, I get a significant result using FDR, but no > significant result using Monte Carlo simulation. How can that be? > > I analyze the sample with the three groups by mri_glmfit. In your > tutorial, I only found how to correct for multiple comparisons with > the Monte Carlo simulation using the command line, but not how to > correct with FDR using the command line. Is there a possibility to do > this? If not, how many iterations are usual to use within the Monte > Carlo simulation? > > Any help is appreciated. > > Thank you very much, > > Marie > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Thanks very much for your help and your advice.
Are there any publications which describe the principles of the Monte Carlo simulation when used for correction of multiple comparisons?
-Marie
2012/6/12 Douglas N Greve greve@nmr.mgh.harvard.edu
yes, though I would probably do it outside of qdec as it can take a while (hours or days)
On 06/12/2012 08:03 AM, Marie Schneider wrote:
Thank you very much for your answer.
Are 10 000 iterations also used when I am running a Monte Carlo simulation in qdec?
Thanks, Marie
2012/6/9 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
they are two different correction schemes. If they gave the same answer, then it would not make sense to have both. the monte carlo tries to compute the probability of a cluster of the given size under the null hypothesis. FDR controls for the number of false positives relative to the total number of positives under the assumption that if any 5% of your positives are false, then you would not change your conclusion.
For monte carlo, we generally use 10000 iterations. If you are using the whole hemisphere, then you can used the cached tables. See the "command-line" tutorial.
doug
On 06/08/2012 08:03 AM, Marie Schneider wrote:
Dear FreeSurfer experts,
I have some questions about corrections for multiple comparisons in FreeSurfer. I have two samples, one consisting of two groups and one consisting of three groups.
I do the comparison with the sample of two groups in qdec.
Correcting
for multiple comparisons, I get a significant result using FDR,
but no
significant result using Monte Carlo simulation. How can that be?
I analyze the sample with the three groups by mri_glmfit. In your tutorial, I only found how to correct for multiple comparisons with the Monte Carlo simulation using the command line, but not how to correct with FDR using the command line. Is there a possibility
to do
this? If not, how many iterations are usual to use within the Monte Carlo simulation?
Any help is appreciated.
Thank you very much,
Marie
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-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Here are a couple Hayasaka 2003 Neuroimage Hagler 2006 Neuroimage The Hagler reg is specifically for surfaces doug
On 06/14/2012 03:13 AM, Marie Schneider wrote:
Thanks very much for your help and your advice.
Are there any publications which describe the principles of the Monte Carlo simulation when used for correction of multiple comparisons?
-Marie
2012/6/12 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
yes, though I would probably do it outside of qdec as it can take a while (hours or days) On 06/12/2012 08:03 AM, Marie Schneider wrote: Thank you very much for your answer. Are 10 000 iterations also used when I am running a Monte Carlo simulation in qdec? Thanks, Marie 2012/6/9 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> they are two different correction schemes. If they gave the same answer, then it would not make sense to have both. the monte carlo tries to compute the probability of a cluster of the given size under the null hypothesis. FDR controls for the number of false positives relative to the total number of positives under the assumption that if any 5% of your positives are false, then you would not change your conclusion. For monte carlo, we generally use 10000 iterations. If you are using the whole hemisphere, then you can used the cached tables. See the "command-line" tutorial. doug On 06/08/2012 08:03 AM, Marie Schneider wrote: > Dear FreeSurfer experts, > > I have some questions about corrections for multiple comparisons in > FreeSurfer. I have two samples, one consisting of two groups and one > consisting of three groups. > > I do the comparison with the sample of two groups in qdec. Correcting > for multiple comparisons, I get a significant result using FDR, but no > significant result using Monte Carlo simulation. How can that be? > > I analyze the sample with the three groups by mri_glmfit. In your > tutorial, I only found how to correct for multiple comparisons with > the Monte Carlo simulation using the command line, but not how to > correct with FDR using the command line. Is there a possibility to do > this? If not, how many iterations are usual to use within the Monte > Carlo simulation? > > Any help is appreciated. > > Thank you very much, > > Marie > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: 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> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
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Marie Schneider