I just realized there wasn't a question in my email below. Is there a way to get a group z-map that is thresholded at some statistically meaningful threshold (ie. cluster size p value) without using mri_glmsim and mri_glmfit? If not, how might I specify a timeseries in the design matrix?
Thank you! Eun Young On Thu, May 5, 2016 at 1:31 PM, Eun Young Choi <cho...@gmail.com> wrote: > Hi Doug, > > Sorry for the confusion. I currently have individual and group mean fcMRI > z-maps from a seed based resting-state analysis (non GLM), but I could also > do a GLM-involved analysis for each subject with the seed's timeseries as a > regressor. My ultimate goal is have a group z-map that is thresholded at > some statistically meaningful threshold. I've tried Bonferroni and FDR > corrections, but they're not stringent enough (i.e., even weak correlations > are highly significant). So I started looking into doing a cluster > size-based correction threshold, which brought me to mri_glmsim and > mri_glmfit. But if there's a way to threshold a group zmap without > mri_glmsim, I could do that. > > Let me know if I can explain further. Thank you! > Eun Young > > > On Thu, May 5, 2016 at 12:22 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> I guess I'm unclear as to what you are trying to do. Are you trying to >> do a time series analysis of the resting state to extract, eg, >> correlation with a seed? Or have you already done your time series >> analysis on each subject, reducing each to a single number at each >> voxel, and now you are doing a group analysis? >> doug >> >> On 05/05/2016 11:44 AM, Eun Young Choi wrote: >> > Thanks, Doug. >> > >> > I'm still a little unclear about how to set up a timeseries regressor >> > (120 timepoints) in the design matrix while also specifying the # of >> > subjects (500). Would the design matrix be a 500x120 or 120x500? >> > >> > I should mention that my ultimate goal is to find a statistically sig. >> > threshold for a cortical fcMRI map with 500 subjects. Traditional >> > correction for multiple comparisons, like Bonferroni and FDR, are not >> > sufficient. So I'd now like to find a cluster size-based correction >> > threshold using mri_glm-sim. Hence, my desire to create the cortical >> > fcMRI map using mri_glmfit, so I can get the files needed for >> > mri_glm-sim. Is this an okay approach, or is there a better way to do >> > this? >> > >> > Thank you so much, >> > Eun Young >> > >> > >> > >> > On Wed, May 4, 2016 at 3:15 PM, Douglas N Greve >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > We don't usually use mri_glmfit for this kind of thing. If you want >> to >> > do it this way, then you cannot use an FSGD file. Instead, create a >> > design matrix with the seed time course then pass that to mri_glmfit >> > with the --X option (and no --fsgd option). >> > >> > On 05/04/2016 10:17 AM, Eun Young Choi wrote: >> > > >> > > Hi all, >> > > >> > > I'd like to run a resting-state fcMRI analysis within the GLM >> > > (mri_glmfit), but I'm not completely sure how to set this up in >> the >> > > FSGD file. I've seen the online tutorial of age vs cortical >> > thickness, >> > > but I'm not sure how to specify a regressor with a timeseries. >> Does >> > > anyone have an example of an FSGD file for this? >> > > >> > > Thanks! >> > > Eun Young >> > > >> > > >> > > >> > > _______________________________________________ >> > > 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 >> > gr...@nmr.mgh.harvard.edu <mailto:gr...@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: 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 <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. >> > >> > >> > >> > >> > -- >> > >> > *Eun Young Choi, PhD* >> > >> > Post-doctoral Associate >> > >> > University of Rochester Medical Center >> > >> > 601 Elmwood Ave, Box 711 >> > >> > Rochester, NY 14642 >> > >> > cell: 551-580-1572 >> > >> > >> > >> > _______________________________________________ >> > 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 >> > > > > -- > > *Eun Young Choi, PhD* > > Post-doctoral Associate > > University of Rochester Medical Center > > 601 Elmwood Ave, Box 711 > > Rochester, NY 14642 > > cell: 551-580-1572 > > -- *Eun Young Choi, PhD* Post-doctoral Associate University of Rochester Medical Center 601 Elmwood Ave, Box 711 Rochester, NY 14642 cell: 551-580-1572
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