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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
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