Hello,
I have encountered a weird error message. It seems that something is wrong with fsl_prepare_fieldmap. I tested the following code line by line and it is only the last line that causes the crash.
${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m
${FSLDIR}/bin/imcp ${PhaseInputName} ${WD}/Phase
${FSLDIR}/bin/fsl_prepare_fieldmap SIEMENS ${WD}/Phase ${WD}/Magnitude_brain ${WD}/FieldMap ${DeltaTE}
When I run it the following appears:
(standard_in) 1: parse error
(standard_in) 1: parse error
(standard_in) 1: parse error
(standard_in) 1: parse error
Loading volumes
Phase loaded
Magnitude loaded
Mask loaded
Rewrapping phase range to [-pi,pi]
Number of phase splits = 8
Calculating starting matrices (709 by 709)
Finished connection_matrices
1150 constraints left
Did while loop 708 times
(standard_in) 1: parse error
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_9LcKmE_tmp_ph_rps
libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
/usr/local/fsl/bin/fsl_prepare_fieldmap: line 194: 54161 Abort trap: 6 $FSLDIR/bin/fslmaths ${tmpnm}_tmp_ph_radians_unwrapped -div $asym ${tmpnm}_tmp_ph_rps -odt float
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_9LcKmE_tmp_ph_rps
libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
/usr/local/fsl/bin/fsl_prepare_fieldmap: line 194: 54164 Abort trap: 6 $FSLDIR/bin/fugue --loadfmap=${tmpnm}_tmp_ph_rps --mask=${maskim} --savefmap=$outfile
Cannot open volume /Users/user/Desktop/FieldMap for reading!
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_9LcKmE_tmp_fmapmasked
Cannot open volume /Users/user/Desktop/FieldMap for reading!
Image Exception : #22 :: ERROR: Could not open image /Users/user/Desktop/FieldMap
libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
/usr/local/fsl/bin/fsl_prepare_fieldmap: line 108: 54168 Abort trap: 6 $FSLDIR/bin/fugue --loadfmap=${outfile} --savefmap=${tmpnm}_tmp_fmapfilt --mask=${maskim} --despike --despikethreshold=2.1
Cannot open volume /tmp/fsl_9LcKmE_tmp_fmapfilt for reading!
Cannot open volume /Users/user/Desktop/FieldMap for reading!
Done. Created /Users/user/Desktop/FieldMap for use with FEAT.
Despite what it says it doesn’t really create /Fieldmap. Do you have any idea of what might be wrong here?
Thanks so much in advance!!