I thought it had to be there because when I don't copy it into the glmdir I get an error message that it can't find the mgh in said glmdir. I'm gonna try running it with the flag you mentioned. What does it mean, though, that it won't compute means over the clusters?
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 26. Mai 2016 17:15:41 Betreff: Re: [Freesurfer] glmdir question
What is it doing in your glmdir? Usually you'd have it in another location when running mri_glmfit (which creates the glmdir). In any case, you can run it with --no-y and it will not look for the input file (and will not compute means over the clusters).
On 5/26/16 8:56 AM, Clara Kühn wrote:
Dear FreeSurfer Experts,
when running the Monte Carlo correction on a GLM I specify this command: mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 --2spaces
This assumes that my mgh file that I used as input for the GLM is in lh.gender_age.glmdir. That means though, that everytime I calculate a GLM and create a new folder for this GLM I have to copy the mgh file into the glmdir to run the Monte Carlo correction. Is there a way to specify where that mgh is located so that I don't have a bunch of copies of it in all my glmdirs?
Thanks for your help! Cheers Clara
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