That should have been --nreps 10000 (not 100:)
On 04/11/2014 11:04 AM, Douglas N Greve wrote:
On 04/11/2014 02:52 AM, Gautam Tammewar wrote:
Hi all,
I'm trying to run Monte Carlo simulations on cortical thickness data I got using mri_glmfit, but I'm running into some errors.
- I used the command
mri_glmfit-sim --glmdir lh.thickness.fwhm20.diagnosis_scanner.dods.glmdir/ --cache 2.0 pos
The error I receive says "cannot find /usr/local/freesurfer_x86_64-5.1.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm40/pos/th20/mc-z.csd"
Even though you've smoothed by 20, the actual FWHM in the data is 40, which is pretty high, and the tables do not go that high. This may indicate that there is something wrong with your data
I'm wondering why the script is looking in the directory "fwhm40" when the data is smoothed using FWHM 20. The directories available under fsaverage/lh/cortex go from fwhm01 to fwhm30.
- Also, for another test I'm running, I created my own average
subjects (instead of using fsaverage). Is there a way to generate the files that are created under /average/mult-comp-cor for this average subject so that I don't have to use the "--sim" flag to run simulations?
Yes, you can use mri_mcsim, something like
mri_mcsim --o /path/to/mult-comp-cor/yoursubject/lh/cortex --base mc-z --save-iter --surf yoursubject lh --nreps 100
This may take several hours or days to run
When running mri_glmfit-sim, add --cache-dir /path/to/mult-comp-cor
doug
Thanks, GT
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