I'm continuing to fine-tune our preFS script for our data, and I'm running into
trouble with the gradient unwarping step. I've obtained the .grad file from our
Skyra scanner and running the HCP with it. It runs the gradient unwarp step,
but seems to fail right after. If I set the GradientDistortionCoeffs variable
in the script to "NONE", the entire script runs without error.
I'm also wondering if this gradient unwarping step is necessary?
Here is the output from the console:
gradunwarp-INFO: Parsing /opt/HCP/coeff_AS098.grad for harmonics coeffs
gradunwarp-INFO: Evaluating spherical harmonics
gradunwarp-INFO: on a 60^3 grid
gradunwarp-INFO: with extents -300.0mm to 300.0mm
gradunwarp-INFO: along x...
gradunwarp-INFO: along y...
gradunwarp-INFO: along z...
gradunwarp-INFO: Evaluating the jacobian multiplier
gradunwarp-INFO: Unwarping slice by slice
gradunwarp-INFO: Writing output to trilinear.nii.gz
Image Exception : #22 :: ERROR: Could not open image
/home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural/analysis/T1w/T1w1_GradientDistortionUnwarp/fullWarp_abs
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/opt/HCP/HCP/global/scripts/GradientDistortionUnwarp.sh: line 92: 11237 Aborted
(core dumped) ${FSLDIR}/bin/convertwarp --abs
--ref=$WD/trilinear.nii.gz --warp1=$WD/fullWarp_abs.nii.gz --relout
--out=$OutputTransform
And the output from the log file:
START: GradientDistortionUnwarp
. . . . . . . . . 10 . . . . . . . . . 20 . . . . . . . . . 30 . . . . . . . .
. 40 . . . . . . . . . 50 . . . . . . . . . 60 . . . . . . . . . 70 . . . . . .
. . . 80 . . . . . . . . . 90 . . . . . . . . . 100 . . . . . . . . . 110 . . .
. . . . . . 120 . . . . . . . . . 130 . . . . . . . . . 140 . . . . . . . . .
150 . . . . . . . . . 160 . . . . . . . . . 170 . . . . . . . . . 180 . . . . .
. . . . 190 . . . . . . . . . 200 . . . . . . . . . 210 . . . . . . . . . 220 .
. . . . . . . . 230 . . . . . . . . . 240 . . . . . . . . . 250 . . . . . . . .
. 260 . . . . . . . . . 270 . . . . . . . . . 280 . . . . . . . . . 290 . . . .
. . . . . 300 . . . . . . . . . 310 . . . . . . . . . 320
set -- --path=/home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural
--subject=analysis
--t1=/home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural/analysis/unprocessed/3T/T1w_MPR1/analysis_3T_T1w_MPR1.nii.gz@
--t2=/home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural/analysis/unprocessed/3T/T2w_SPC1/analysis_3T_T2w_SPC1.nii.gz@
--t1template=/opt/HCP/HCP/global/templates/MNI152_T1_0.7mm.nii.gz
--t1templatebrain=/opt/HCP/HCP/global/templates/MNI152_T1_0.7mm_brain.nii.gz
--t1template2mm=/opt/HCP/HCP/global/templates/MNI152_T1_2mm.nii.gz
--t2template=/opt/HCP/HCP/global/templates/MNI152_T2_0.7mm.nii.gz
--t2templatebrain=/opt/HCP/HCP/global/templates/MNI152_T2_0.7mm_brain.nii.gz
--t2template2mm=/opt/HCP/HCP/global/templates/MNI152_T2_2mm.nii.gz
--templatemask=/opt/HCP/HCP/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz
--template2mmmask=/opt/HCP/HCP/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
--brainsize=150
--fnirtconfig=/opt/HCP/HCP/global/config/T1_2_MNI152_2mm.cnf
--fmapmag=/home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural/analysis/unprocessed/3T/T1w_MPR1/analysis_3T_FieldMap_Magnitude.nii.gz
--fmapphase=/home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural/analysis/unprocessed/3T/T1w_MPR1/analysis_3T_FieldMap_Phase.nii.gz
--echodiff=2.46 --SEPhaseNeg=NONE --SEPhasePos=NONE
--echospacing=NONE --seunwarpdir=NONE \
--t1samplespacing=0.0000065 --t2samplespacing=0.0000023
--unwarpdir=z --gdcoeffs=/opt/HCP/coeff_AS098.grad
--avgrdcmethod=FIELDMAP --topupconfig=NONE --printcom=
. /opt/HCP/HCP/Examples/Scripts/SetUpHCPPipeline.sh
_________________________________________________
Gregory Book
Senior Technology Manager
Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital
200 Retreat Avenue
Hartford, CT 06106
Tel: 860-545-7267 Fax: 860-545-7797
[email protected]<mailto:[email protected]>
http://nidb.sourceforge.net
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