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Hi Dr. Greve, hi all

I have tried your code. I copied it from the website into a text file and replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable but aborts after a few lines with no indication of a cause. The following output is generated:


xx@xxx:~/Schreibtisch/WMH_DCS$ mri_glmfit-sim --glmdir rh.volume.DCS.10.glmdir --cache 2.3 abs --cwp 0.05 --2spaces --spatial-sum
cmdline mri_glmfit.bin --y rh.volume.DCS.10.mgh --fsgd FSGD/DCSstudy.fsgd --C Contrasts/DCS-DCSK.mtx --C Contrasts/DCSK-DCS.mtx --surf fsaverage rh --cortex --glmdir rh.volume.DCS.10.glmdir
SURFACE: fsaverage rh
Unmatched `.


Even if I run --help, only some of the lines appear:

mri_glmfit-sim --help

 --glmdir glmdir
 --cwp cwthresh : cluster-wise p-value threshold (.05)

Use pre-computed z-based monte-carlo simulations (see mri_mcsim)
 --mczsim vwthreshold sign
If you have run your own simulations (mri_mcsim), then specify
   --mczsim-dir dir : default is FREESURFER_HOME/average/mult-comp-cor
   --mczsim-label label : default is cortex

Use permutation simulation
 --perm nsim CFT sign : permutation simulation with nsim iterations
Unmatched ".


Do you have any idea why this might be?
Like Xiaoxu before me, I have already tried to convert the file with dos2unix. However, without the desired effect.

I am using Linux Ubuntu 16.04 and Freesurfer Vers. 6.0.

I would be very grateful for any tips.

Best regards


sven