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 <greve@nmr.mgh.harvard.edu mailto:greve@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 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: 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
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