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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://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528... and in the known issues list of v5.3. here https://surfer.nmr.mgh.harvard.edu/fswiki/PreviousReleaseNotes.
We have libcrypt version 2.17 installed and do not have access to libcrypt-2.14.1.so. Is there a way to get libcrypt-2.14.1.so from you or is there another known workaround (other then updating to Freesurfer 6)?
Thank you very much! Caspar
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://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528...
and in the known issues list of v5.3. here https://surfer.nmr.mgh.harvard.edu/fswiki/PreviousReleaseNotes.
We have libcrypt version 2.17 installed and do not have access to libcrypt-2.14.1.so http://libcrypt-2.14.1.so. Is there a way to get libcrypt-2.14.1.so http://libcrypt-2.14.1.so from you or is there another known workaround (other then updating to Freesurfer 6)?
Thank you very much! Caspar
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 CautionHi! 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.ed...
and in the known issues list of v5.3. here
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.... .
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&...
. 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&...
from you or is there another known workaround (other then updating to Freesurfer 6)?
Thank you very much! Caspar
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
freesurfer@nmr.mgh.harvard.edu
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Caspar M. Schwiedrzik -
Greve, Douglas N.,Ph.D.