#!/bin/tcsh -f
#SBATCH --time=300:00:00
#SBATCH --mem=24000
#SBATCH --output=results
#SBATCH --cores=6
set subj= ($argv[1])
trac-preproc -c /homes/dcallow/dti_freesurf/trac/Ex.${subj}.long.base_${subj}/scripts/dmrirc.local -log /homes/dcallow/dti_freesurf/trac/Ex.${subj}.long.b$
trac-preproc -c /homes/dcallow/dti_freesurf/trac/Rest.${subj}.long.base_${subj}/scripts/dmrirc.local -log /homes/dcallow/dti_freesurf/trac/Rest.${subj}.lo$
trac-preproc -c /homes/dcallow/dti_freesurf/trac/base_${subj}/scripts/dmrirc.local -log /homes/dcallow/dti_freesurf/trac/base_${subj}/scripts/trac-all.log$
changing the input for ${subj} for each subject I run I get the following error.
FileName /homes/dcallow/diffusion_recons//AES137.Ex/image000001.dcm
Identification
syngo MR B17 N
umarisVeScannerModel TrioTimPatientName Date and time
20180119 S
tudyDateStudyTime 103151.312000
SeriesTime 113039.437000
AcqTime 113030.842500
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 169
SeriesNo 170
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65 NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 106.0489 107.8193 -44.0513
VolRes 1.6406 1.6406 3.6000
VolDim 128
128 Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 1.0489 2.8193 18.9487
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0 1
INFO: no Siemens slice order reversal detected (good!).
TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES136/dmri/dwi_orig.nii.gz...
Saving bvals and bvecs
mv -f /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES136/dmri/dwi_orig.voxel_space.bvecs /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES$
mri_probedicom --i /homes/dcallow/diffusion_recons//AES136.Ex/image000001.dcm > /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES136/dmri/dcminfo.d$
mv -f /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES136/dmri/bvecs.tmp /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES136/dmri/dwi_orig$
R=6300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
Reslicing using nearest
writing to /homes/dcallow/dti_freesurf/trac/Rest.AES127.long.base_AES127/dmri/dwi_orig_las.nii.gz...
INFO: found /homes/dcallow/dti_freesurf/trac/Rest.AES127.long.base_AES127/dmri/dwi_orig.bvals, copying
INFO: found /homes/dcallow/dti_freesurf/trac/Rest.AES127.long.base_AES127/dmri/dwi_orig.bvecs, converting to LAS
mv -f /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base_AES120/dmri/dwi_orig_las.bvecs /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base_AES120/$mv -f /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base_AES120/dmri/dwi_orig_las.bvals /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base_AES120/$eddy_correct /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base_AES120/dmri/dwi_orig_las.nii.gz /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base$9/sys:/cell_root/software/fsl/new/sys/bin/remove_ext: No such file or directory
/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 87: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 87: [: -eq: unary operator expected
Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
fslroi <input> <output> <tmin> <tsize>
fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize>
Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension.
Cannot open volume _tmp for reading!
/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 95: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$
Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
/bin/rm: cannot remove `_tmp????.*': No such file or directory
/bin/rm: cannot remove `_ref*': No such file or directory
/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 83: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/
ys:/cell_root/software/fsl/new/sys/bin/remove_ext: No such file or directory
/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 84: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 87: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 87: [: -eq: unary operator expected
Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
fslroi <input> <output> <tmin> <tsize>
fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize>
Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension.
Cannot open volume _tmp for reading!
/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 95: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$
Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
/bin/rm: cannot remove `_tmp????.*': No such file or directory
/bin/rm: cannot remove `_ref*': No such file or directory
trac-preproc exited with ERRORS at Fri Apr 19 15:45:56 EDT 2019
Any idea why the script might be throwing this error?
Best,
Daniel CallowPhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
443-254-6298