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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 <svku...@gmx.de>
*Sent:* Saturday, February 10, 2024 5:09 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Huang,
Yujing <yhuan...@mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Unit of the Numbers in
cache.th40.neg.y.ocn.dat
* External Email - Use Caution *
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
$FREESURFER_HOME/bin/mri_glmfit-sim –help”? I’m hoping it will
give some hints.
Best,
Yujing
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of
*Sven Kühn
*Sent:* Sunday, February 4, 2024 12:09 PM
*To:* Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Unit of the Numbers in
cache.th40.neg.y.ocn.dat
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Hi Dr. Greve, hi all
I have tried your code. I copied it from the website into a text
file and replaced mri_glmfit-sim in the freesurfer/bin folder. The
file is executable but aborts after a few lines with no indication
of a cause. The following output is generated:
/xx@xxx:~/Schreibtisch/WMH_DCS$ 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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