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Hello,
After running
trac-all -prep -jobs file -c /homes/dcallow/dmrirc.long.example.parallel.sh
I am trying to submit the jobs for parallel computing.
However, when running the following
#!/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 Linux compute-4-28.bswift.umd.edu 2.6.32-696.30.1.el6.x86_64 #1 SMP Fri May 18 11:50:44 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux
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 Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298