Re: [Freesurfer] Resting-state fcMRI analysis with GLM

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
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>

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--

*Eun Young Choi, PhD*

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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 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/

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