I see the problem.

In ‘usage_exit:’ section, you will notice several echo statements are split into two lines. Fix those lines and try again. ‘“tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help” will help you identify those lines.

Best,

Yujing

From: Sven Kühn <svkuehn@gmx.de>
Sent: Saturday, February 10, 2024 5:09 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Huang, Yujing <YHUANG43@mgh.harvard.edu>
Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

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Many thanks for the answer! Sorry, there seems to be some context missing. I was replying to an old post from the archives and thought it would attach itself there. I copied the script for mri_glmfit-sim from that post.
Here is the link to it:

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I think the mistake is that I didn't convert it into a script properly. Could you perhaps provide me with the script as a file? I would like to get the volume of each subject from the ocn.dat by adding --spatial-sum to the command line. Exactly as described in the post.

Best

Sven

Am 06.02.24 um 15:16 schrieb Huang, Yujing:

I can’t reproduce the error here with FS 6.0. Not sure where you downloaded the script. Can you run this “tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help”? I’m hoping it will give some hints.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Sven Kühn
Sent: Sunday, February 4, 2024 12:09 PM
To: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

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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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