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Hello Caspar, So are you saying that if you run directly from the terminal in bash (or maybe in csh with % sign as prompt) $ mri_convert -i inputvolume.mgz --out_orientation LPS -iis .5 -ijs .5 -iks .5 -vs 1.2 1.2 1.2 - that the command works, but it does not work when run from within a csh script ? If you are getting different results from running commands in the terminal environment/shell compared to when the same command runs in a script, there must be something different between the terminal and the script shell environment, e.g. LD_LIBRARY_PATRH, PATH, or something getting set differently. I would try and reproduce the shell environment variable settings that work from the terminal in the csh script. You could try explicitly running the csh script with -xf as arguments (prints out what is getting executed and bypasses any startup settings) to see if it works differently.   You can replace foo.csh with your script name below. $ csh -xf  foo.csh Another useful thing to do is to look at all the environment variables getting set in the terminal window where the command works, via $ env | sort - and compare that with what you see the csh script sets in the output of “csh -xf foo.csh”.  You can put an “env | sort” command in the csh script just before the mri_convert command runs to see the environment (and then compare it to the output of :”env | sort” in the terminal window where the command works). 

- R.         External Email - Use CautionHi!Unfortunately, it turns out that downgrading glibc does not solve this issue, neither with .14 nor with .15 versions.Doug, we are calling mri_convert from a csh script, with the following options:mri_convert -i inputvolume.mgz -o outputvolume.nii.gz --out_orientation LPS -iis .5 -ijs .5 -iks .5 -vs 1.2 1.2 1.2We then simply get segmentation fault (core dumped).It seems to work when we run the same command directly in the terminal.CasparAm Do., 16. Mai 2019 um 23:10 Uhr schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>:   Can you send the command line and full terminal output?   On 5/16/19 5:17 AM, Caspar M. Schwiedrzik wrote:        External Email - Use CautionHi!We are getting segmentation fault (core dumped) error when trying torun mri_convert on NIFTI files. This is running Freesurfer v5.3 onCentos6, specifically v1.179.2.7 of mri_convert.I suspect that this has to do with libcrypt incompatibilitiesdescribed for other operating systems , e.g., here:   https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh..harvard.e... in the known issues list of v5.3. here   https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.... have libcrypt version 2.17 installed and do not have access tolibcrypt-2.14.1.so <http://libcrypt-2..14.1.so%3E%C2%A0%C2%A0%C2%A0%3Chttps://urldefense.proofpo... there a way to get libcrypt-2.14.1.so   <http://libcrypt-2.14.1.so%3E%C2%A0%C2%A0%C2%A0%3Chttps://urldefense.proofpoi... you or is there another known workaround (other then   updating toFreesurfer 6)?Thank you very much! Caspar_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu   <mailto:Freesurfer@nmr.mgh.harvard.edu>   https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... mailing list   Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>   https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... Message Part.txt>