Re: [Freesurfer] adapt Monte Carlo correction for specific sample

Thanks a lot! I will do that then :)

Cheers, Clara

----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 15. März 2016 17:40:08 Betreff: Re: [Freesurfer] adapt Monte Carlo correction for specific sample

You can just store it in a different directory, then use the --cache-dir option when running mri_glmfit-sim to specify the new folder, eg, if you use --o /path/to/myspace/yoursubject/lh/cortex, then specify /path/to/myspace

On 03/15/2016 12:36 PM, Clara Kühn wrote:

Dear FreeSurfer experts,

I have a question regarding the Monte Carlo correction. To create a Monte Carlo correction for my specific sample (4year old kids) the wiki suggests this command: mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/lh/cortex --base mc-z --surface yoursubject lh --nreps 10000

I have run this command, however I get an error message that I have no rights to write into the $FREESURFER_HOME directory. I work at an institute where that directory is stored on a server to which many people have access but no writing rights (which is definitely a good thing), so getting the rights is not really an option. I was wondering now whether I could just specify a different directory or whether it absolutely has to be the $FREESURFER_HOME directory? If the latter is the case, would you suggest I install a local copy or do you have any other suggestions?

Thanks in advance! Clara

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