[Freesurfer] fsgd
Dear FreeSurfer experts, I am trying to start mris_preproc, but unfortunately it doesn't find my created fsgd file. I saved it in the foulder where you can find all subjects data. Shall I save it somewhere else? Thanks for your help, best Marie ___ 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.
Re: [Freesurfer] fsgd
I exactly tried that. I typed: mris_preproc --fsgd \ --cache in thickness.fwhm.10.fsaverage \ --target fsaverage \ --hemi lh \ --out .mgh everytime I am running this it says that my fsgd file cannot be found. So I wonder where I have to save it so that FreeSurfer can find it. Thanks for any help Marie 2012/6/6 Douglas Greve > Hi Marie, you have to pass it as a command-line option with --fsgd > doug > > > On 6/6/12 4:19 AM, Marie Schneider wrote: > > Dear FreeSurfer experts, > > I am trying to start mris_preproc, but unfortunately it doesn't find my > created fsgd file. I saved it in the foulder where you can find all > subjects data. Shall I save it somewhere else? > > Thanks for your help, > > best Marie > > ___ > Freesurfer mailing > listfreesur...@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. > > ___ 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] correction for multiple comparisons
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 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.
Re: [Freesurfer] correction for multiple comparisons
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 > 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 1 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 > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > ___ > 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 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.
Re: [Freesurfer] correction for multiple comparisons
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 > 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 > gr...@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 1 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:freesur...@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 >>gr...@nmr.mgh.harvard.edu >> <mailto:gr...@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> >> >> <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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >>__**_ >>Freesurfer mailing list >>Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@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 >&
[Freesurfer] (no subject)
Dear FreeSurfer expects, I ran a cortical thickness analysis that revealed many significant clusters, but half of them are pretty small. Is there a possibility in qdec to display only clusters with a certain clustersize on the inflated surface? Thank you very much for your help, best wishes, Marie ___ 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.
