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Thank you very much! Everything went well. I went through the script and was able to find some lines that were split. After I found them all, everything worked.
Thanks again!
Am 14.02.24 um 21:56 schrieb Huang, Yujing:
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 $FREESURFER_HOME/bin/mri_glmfit-sim –help”? I’m hoping it will give some hints. Best, Yujing *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Sven Kühn *Sent:* Sunday, February 4, 2024 12:09 PM *To:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat * External Email - Use Caution * Hi Dr. Greve, hi all I have tried your code. I copied it from the website into a text file and replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable but aborts after a few lines with no indication of a cause. The following output is generated: /xx@xxx:~/Schreibtisch/WMH_DCS$ 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. 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