trac-all running -jobs issue error - Freesurfer

19 Apr 2019


      External Email - Use Caution
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