fsl_prepare_fieldmap is an unmodified FSL script that is called by the HCP
Pipelines. I would ask on the FSL mailing list about that. You could try
testing that script outside of the HCP Pipelines by using these commands line
on the files:
${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m #Brain
extract the magnitude image
${FSLDIR}/bin/imcp ${PhaseInputName} ${WD}/Phase
${FSLDIR}/bin/fsl_prepare_fieldmap SIEMENS ${WD}/Phase ${WD}/Magnitude_brain
${WD}/FieldMap ${DeltaTE}
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Vanessa K
<vanessakr1...@gmail.com<mailto:vanessakr1...@gmail.com>>
Date: Thursday, April 6, 2017 at 2:53 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Error during Field Map Preprocessing and Gradient
Unwarping in the Functional Volume Pipeline
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
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
