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Hi!
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 1.2

We then simply get segmentation fault (core dumped).
It seems to work when we run the same command directly in the terminal.
Caspar


Am Do., 16. Mai 2019 um 23:10 Uhr schrieb Greve, Douglas N.,Ph.D. <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 Caution
>
> Hi!
> We are getting segmentation fault (core dumped) error when trying to
> run mri_convert on NIFTI files. This is running Freesurfer v5.3 on
> Centos6, specifically v1.179.2.7 of mri_convert.
>
> I suspect that this has to do with libcrypt incompatibilities
> described for other operating systems , e.g., here:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail__freesurfer_2014-2DSeptember_040528.html&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s&s=hvSTVmJcAZKj26WCCcgZbqDQcLE9GL1yLaGOXIcGBEY&e=
>
> and in the known issues list of v5.3. here
> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_PreviousReleaseNotes&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s&s=PUDfyokNDX6MKj07m6SVKp-n_mHLc-wsBpe1nedrdD8&e=.
>
> We have libcrypt version 2.17 installed and do not have access to
> libcrypt-2.14.1.so <https://urldefense.proofpoint.com/v2/url?u=http-3A__libcrypt-2D2.14.1.so&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s&s=oWqfVu5YGSWScZMw3Ypfdy53osHoNywLPtAffB75oR8&e=>.
> Is there a way to get libcrypt-2.14.1.so <https://urldefense.proofpoint.com/v2/url?u=http-3A__libcrypt-2D2.14.1.so&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=NBmjYrhl1nTR7-ra_mfc3mtbFAElda33iU_qYFc-17s&s=oWqfVu5YGSWScZMw3Ypfdy53osHoNywLPtAffB75oR8&e=>
> from you or is there another known workaround (other then updating to
> Freesurfer 6)?
>
> Thank you very much! Caspar
>
>
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