I’m posting my question here, because I got the exact same error message and followed the error solving steps provided here. Everything the same: same content in my first_flirt.o36681 and my first.o* files.
However, my first_flirt.e36681 is empty…
I checked of course if I have the MNI152lin_T1_1mm_subbr_mask and I do.
My first.e* files give me the following error message
$ more first.e*
::::::::::::::
first.e47902.1
::::::::::::::
terminate called after throwing an instance of 'NEWMAT::SingularException'
/usr/local/fsl/bin/run_first: line 164: 47975 Aborted (core dumped) ${FSLDIR}/bin/first -i $i
mage -l $trmat -m $model -k $outname -n $modes $verbose $comExtras
::::::::::::::
first.e47902.10
::::::::::::::
terminate called after throwing an instance of 'NEWMAT::SingularException'
/usr/local/fsl/bin/run_first: line 164: 1965 Aborted (core dumped) ${FSLDIR}/bin/first -i $i
mage -l $trmat -m $model -k $outname -n $modes $verbose $comExtras
::::::::::::::
first.e47902.2
::::::::::::::
Would be grateful for some help on figuring this out!
Thanks,
Steph
PS.: I tried both unset SGE_ROOT as well as
SGE_ROOT="" 5ttgen fsl T1.coreg.nii 5tt_act.mif as suggested by @jdtournier here 5ttgen 'run_first_all' error and still got the same error including the same message that
5ttgen: FSL FIRST job has been submitted to SGE; awaiting completion which then never completes…