Dear users,
I am not sure whether I should turn to you or to the FSL mailing list, but
I will try my luck here first. I suspect it has something to do with
filling in values in the GenericfMRIVolumeProcessingPipelineBatch.sh script
(because of the illegal characters almost spelling "NONE" and it
complaining that the dwell time is set to NONE). You can see my settings on
the bottom. The error message is this:
"END: Field Map Preprocessing and Gradient Unwarping
(standard_in) 1: illegal character: N
(standard_in) 1: illegal character: O
(standard_in) 1: illegal character: N
(standard_in) 1: illegal character: N
(standard_in) 1: illegal character: O
(standard_in) 1: illegal character: N
/home/guestuser/Desktop/lisa/Pipelines/global/scripts/epi_reg_dof: line
182: [: =: unary operator expected
Running FAST segmentation
FLIRT pre-alignment
Registering fieldmap to structural
Running BBR with fieldmap
0.482078 0.999999 -0.000744 -0.001198 0.000000 0.000738 0.999984 -0.005527
0.000000 0.001202 0.005526 0.999984 0.000000 0.157694 2.242522 5.317938
1.000000
Making warp fields and applying registration to EPI series
Part of FSL (build 509)
fugue
FMRIB's Utility for Geometric Unwarping of EPIs
Copyright(c) 2000-2008, University of Oxford (Mark Jenkinson)
Usage:
fugue -i <epi> -p <unwrapped phase map> -d <dwell-to-asym-ratio> -u
<result> [options]
fugue -i <unwarped-image> -p <unwrapped phase map> -d
<dwell-to-asym-ratio> -w <epi-like-result> [options]
fugue -p <unwrapped phase map> -d <dwell-to-asym-ratio>
--saveshift=<shiftmap> [options]
Optional arguments (You may optionally specify one or more of):
-i,--in filename of input volume
-u,--unwarp apply unwarping and save as filename
-w,--warp apply forward warp and save as filename
-p,--phasemap filename for input phase image
-d,--dwelltoasym set the dwell to asym time ratio
--dwell set the EPI dwell time per phase-encode line - same as echo
spacing - (sec)
--asym set the fieldmap asymmetric spin echo time (sec)
--savefmap filename for saving fieldmap (rad/s)
--loadfmap filename for loading fieldmap (rad/s)
--saveshift filename for saving pixel shift volume
--loadshift filename for reading pixel shift volume
-m,--median apply 2D median filtering
--despike apply a 2D de-spiking filter
--nofill do not apply gap-filling measure to the fieldmap
--noextend do not apply rigid-body extrapolation to the fieldmap
--smooth2 apply 2D Gaussian smoothing of sigma N (in mm)
-s,--smooth3 apply 3D Gaussian smoothing of sigma N (in mm)
--poly apply polynomial fitting of order N
--fourier apply Fourier (sinusoidal) fitting of order N
--pava apply monotonic enforcement via PAVA
--despikethreshold specify the threshold for de-spiking (default=3.0)
--unwarpdir specifies direction of warping [x/y/z/x-/y-/z-] (default
y)
--phaseconj apply phase conjugate method of unwarping
--icorr apply intensity correction to unwarping (pixel shift method
only)
--icorronly apply intensity correction only (must specify output
with -u,--unwarp)
--mask filename for loading valid mask
--unmaskfmap saves the unmasked fieldmap when using --savefmap
--unmaskshift saves the unmasked shiftmap when using --saveshift
--nokspace do not use k-space forward warping
--nocheck turn off all checking
-v,--verbose switch on diagnostic messages
-h,--help display this message
--dwell: Couldn't set_value! valstr="NONE"!
Image Exception : #22 :: ERROR: Could not open image
/media/662A63022A62CE9D/lisa/StudyDirectory/008/rfMRI_REST1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted_fieldmaprads2epi_shift
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/guestuser/Desktop/lisa/Pipelines/global/scripts/epi_reg_dof: line
386: 149158 Aborted (core dumped) $FSLDIR/bin/convertwarp
-r ${vrefhead} -s ${vout}_fieldmaprads2epi_shift --postmat=${vout}.mat -o
${vout}_warp --shiftdir=${fdir} --relout
Image Exception : #22 :: ERROR: Could not open image
/media/662A63022A62CE9D/lisa/StudyDirectory/008/rfMRI_REST1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted_warp
An error occured while reading file:
/media/662A63022A62CE9D/lisa/StudyDirectory/008/rfMRI_REST1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted_warp
Image Exception : #22 :: ERROR: Could not open image
/media/662A63022A62CE9D/lisa/StudyDirectory/008/rfMRI_REST1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted_warp
An error occured while reading file:
/media/662A63022A62CE9D/lisa/StudyDirectory/008/rfMRI_REST1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted_warp.nii.gz
set -- --path=/media/662A63022A62CE9D/lisa/StudyDirectory
--subject=008 --fmriname=rfMRI_REST1
--fmritcs=/media/662A63022A62CE9D/lisa/StudyDirectory/008/unprocessed/3T/rfMRI_REST1/008_3T_rfMRI_REST1.nii.gz
--fmriscout=NONE --SEPhaseNeg=NONE --SEPhasePos=NONE
--fmapmag=/media/662A63022A62CE9D/lisa/StudyDirectory/008/unprocessed/3T/rfMRI_REST1/008_rfMRI_REST1_FieldMap_Magnitude.nii
--fmapphase=/media/662A63022A62CE9D/lisa/StudyDirectory/008/unprocessed/3T/rfMRI_REST1/008_rfMRI_REST1_FieldMap_Phase.nii
--fmapgeneralelectric=NONE --echospacing=NONE
--echodiff=2.46 --unwarpdir=-y --fmrires=2
--dcmethod=FIELDMAP --gdcoeffs=NONE --topupconfig=NONE
--printcom= --biascorrection=NONE --mctype=MCFLIRT
Any ideas of what can be wrong?
Thanks a lot!
Lisa
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