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
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