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:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg68973.htmlhttps://secure-web.cisco.com/1C0tWp9a2AtgW6pz_K_YQQcl2gRLBm9YoGcFQf6OVnEWfU4xw_g9pNGtHahFmsjDHViYZcmLpx46sC-hnSXa_-HO_SWPh8Rn69JL37CIR4BjCC2U3i4xsmKBMaXA4_fmUDv9NRW_O_bKJKzfaVrQC37KFNK6gZM67pA5BkW2Ex3X4Q5zL3-hcBKuwPldhBY6uZ4u0mS_5yi_DNx3l0Te4GrqRDFTtFiqWBLEESSTbjtSiQQqKooQRy9pyYoJ61tWb3JVMXq7WAbovDlQzXcpt-kYgTcG3RPZ3ywYqskFJEZhEebype-G7ouR1yX1s4lLa/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg68973.html
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 $FREESURFER_HOME/bin/mri_glmfit-sim –help”? I’m hoping it will give some hints.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Sven Kühn Sent: Sunday, February 4, 2024 12:09 PM To: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
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Hi Dr. Greve, hi all
I have tried your code. I copied it from the website into a text file and replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable but aborts after a few lines with no indication of a cause. The following output is generated:
xx@xxx:~/Schreibtisch/WMH_DCS$ 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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