Hello,
I encountered a weird error while trying to run the FunVol Pipeline. After
the motion correction is done I get this:
START: Field Map Preprocessing and Gradient Unwarping
(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_EgzoAc_tmp_ph_rps
libc++abi.dylib: terminating with uncaught exception of type
RBD_COMMON::BaseException
/usr/local/fsl/bin/fsl_prepare_fieldmap: line 194: 52721 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_EgzoAc_tmp_ph_rps
libc++abi.dylib: terminating with uncaught exception of type
RBD_COMMON::BaseException
/usr/local/fsl/bin/fsl_prepare_fieldmap: line 194: 52723 Abort trap: 6
$FSLDIR/bin/fugue --loadfmap=${tmpnm}_tmp_ph_rps --mask=${maskim}
--savefmap=$outfile
Cannot open volume
/Users/user/Desktop/StudyDirectory/002/rfMRI_REST/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/FieldMap
for reading!
Image Exception : #22 :: ERROR: Could not open image
/tmp/fsl_EgzoAc_tmp_fmapmasked
Cannot open volume
/Users/user/Desktop/StudyDirectory/002/rfMRI_REST/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/FieldMap
for reading!
Image Exception : #22 :: ERROR: Could not open image
/Users/user/Desktop/StudyDirectory/002/rfMRI_REST/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/FieldMap
libc++abi.dylib: terminating with uncaught exception of type
RBD_COMMON::BaseException
/usr/local/fsl/bin/fsl_prepare_fieldmap: line 108: 52727 Abort trap: 6
$FSLDIR/bin/fugue --loadfmap=${outfile}
--savefmap=${tmpnm}_tmp_fmapfilt --mask=${maskim} --despike
--despikethreshold=2.1
Cannot open volume /tmp/fsl_EgzoAc_tmp_fmapfilt for reading!
Cannot open volume
/Users/user/Desktop/StudyDirectory/002/rfMRI_REST/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/FieldMap
for reading!
Done. Created
/Users/user/Desktop/StudyDirectory/002/rfMRI_REST/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/FieldMap
for use with FEAT.
DONE: fsl_prepare_fieldmap.sh
cp:
/Users/user/Desktop/StudyDirectory/002/rfMRI_REST/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/FieldMap.nii.gz:
No such file or directory
set -- --path=/Users/user/Desktop/StudyDirectory --subject=002
--fmriname=rfMRI_REST
--fmritcs=/Users/user/Desktop/StudyDirectory/002/unprocessed/3T/rfMRI_REST/002_3T_rfMRI_REST.nii
--fmriscout=NONE --SEPhaseNeg=NONE --SEPhasePos=NONE
--fmapmag=/Users/user/Desktop/StudyDirectory/002/unprocessed/3T/rfMRI_REST/002_3T_rfMRI_REST_FieldMap_Magnitude.nii
--fmapphase=/Users/user/Desktop/StudyDirectory/002/unprocessed/3T/rfMRI_REST/002_3T_rfMRI_REST_FieldMap_Phase.nii
--fmapgeneralelectric=NONE --echospacing=NONE
--echodiff=2.46ms --unwarpdir=-y --fmrires=2
--dcmethod=SiemensFieldMap --gdcoeffs=NONE --topupconfig=NONE
--printcom= --biascorrection=NONE --mctype=MCFLIRT
.
/Users/user/Desktop/hcp/Pipelines-3.22.0-beta.5/Examples/Scripts/SetUpHCPPipeline.sh
This looks very confusing, do you have any idea why is it so? At first I
thought fsl 5.0.9 might be the problem, but even with 5.0.6 the problem
persists. Also in the /tmp/ folder there are the files it can't open. I am
using DistortionCorrection="SiemensFieldMap" and the only fields which are
not set to "NONE" are Magnitude and Phase input names, Task and Phase
encoding list, DeltaTE and final resolution.
Thanks so much in advance!
Vanessa
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