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 <greve@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
> <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
>     >
>     >
>     >
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>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
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> *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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--
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/BugReporting
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--

Eun Young Choi, PhD

Post-doctoral Associate

University of Rochester Medical Center

601 Elmwood Ave, Box 711

Rochester, NY 14642

cell: 551-580-1572