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
