Thanks Doug - so the residual file would be [number of subjects x number of vertices] matrix? Does it have to be in special file format?

> So you will generate the sig.mgh file? I would recommend just running 
> mri_glmfit using a design close to whatever you did to generate the 
> directory structure, then just replace the sig.mgh file with the file of 
> your choosing. The one snag may be the fwhm.dat file. This is a measure 
> of the spatial correlation in the residual. Since it works off the 
> residual, it depends on the actual design. If your analysis produces a 
> residual, you can run mris_fwhm to get the fwhm.dat file, and then just 
> run mri_glmfit-sim.

> doug

> On 06/02/2016 02:56 PM, Chung, Yoonho wrote:
>
> Dear experts,
>
>
> This is a follow-up question from my previous post.
>
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47287.html
>
>
> If I am running stats with my own stats code to generate p-values and 
> other parameters, what other files
>
> do I need to generate in order to run 'mri_glmfit-sim'? I do not have 
> the glmdir file (since I am not running mri_glmfit) so I would like to 
> know which files need to be supplied with which flag/option, in place 
> of the '--glmdir', for mri_glmfit-sim to run the cluster-based 
> correction for my vector of p-values. An example command would be 
> extremely helpful. Thank you in advance!
>
>
> Best,
>
> Yoon