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:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg68973.html<https://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 $FREESURFER_HOME/bin/mri_glmfit-sim –help”?
I’m hoping it will give some hints.
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
On Behalf Of Sven Kühn
Sent: Sunday, February 4, 2024 12:09 PM
To: Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>;
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
External Email - Use Caution
Hi Dr. Greve, hi all
I have tried your code. I copied it from the website into a text file and
replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable
but aborts after a few lines with no indication of a cause. The following
output is generated:
xx@xxx:~/Schreibtisch/WMH_DCS$ 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.
Best regards
sven
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