[Freesurfer] QDEC - command not found

[Alba Castells Sánchez]

External Email - Use Caution

Dear freesurfer experts,
we installed the last version of freesurfer dev in a centos7 system (8th
january 2019) and the matlab runtime to run segmentHA_T1.sh. We could
obtain all the files without problems.

However, today we tried to open qdec typing qdec like we used to do with
other versions without problem and the answer is "command not found". We
are really surprised, we haven't found any other comment on internet and
the mailing list with this same problem.

We have installed the same last version in a mac and we had the same
problem. qdec doesn't exist.

We have checked the files .sh  in Freesurfersetup  and similar files in the
freesurfer direcotry looking for qdec without success. HOwever, there is a
direcotry called Qdec in freesurfer/matlab/lme

We don't know where is our mistake.
We are also considering that maybe the issue is related with the version.
Is this possible?
Could you help us, please?

Thousand thanks
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] HIPPOCAMPUS AND AMYGDALA SEGMENTATION - Invalid MEX-file

[Alba Castells Sánchez]

External Email - Use Caution

Dear Freesurfer experts,

We installed today (8 jan 2019) the last version of Freesurfer dev and the
corresponding Runtime Matlab R2014b .
We tried segmentHA_T1.sh with bert to check if it worked.
We had a couple of errors related to an Invalid Mex-file. We add the log.
We doubt if it may be related to the fact that our computer is not updated
to OS El Capitan and we are using OS High Sierra. It is something very
simple but we hadn’t realized until now or wether is something to the
software.

Could you help us?
Thousand thanks!


#
#@# Hippocampal Subfields processing (T1) left martes,  8 de enero de 2019,
18:25:06 CET
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:
Invalid MEX-file
'/tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64':
dlopen(/tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64,
6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
  Referenced from:
/tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64
  Expected in: /usr/lib/libstdc++.6.0.9.dylib
 in
/tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64

Error in kvlClear (line 11)



Error in segmentSubjectT1_autoEstimateAlveusML (line 115)



MATLAB:invalidMEXFile
Darwin MacBook-Air-de-Francesca.local 17.7.0 Darwin Kernel Version 17.7.0:
Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64

T1 hippocampal subfields exited with ERRORS at martes,  8 de enero de 2019,
18:25:19 CET

For more details, see the log file
/Applications/freesurfer/subjects/bert/scripts/hippocampal-subfields-T1.log
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer