Hi Martin,
Thank you. I am able to open up the gui but now am running into errors with the preview and also with other processing. It seems to be specific to the tmp folders created - they can't be found). Any ideas? Error messages below:
When trying to preview in the GUI:
Traceback (most recent call last):
File "/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/python/asl/gui/run_box.py", line 183, in get_preview_data
img = nib.load(meanfile)
File "/home/apps/fsl-5.0.11/fslpython/envs/fslpython/lib/python3.6/site-packages/nibabel/loadsave.py", line 40, in load
raise FileNotFoundError("No such file: '%s'" % filename)
FileNotFoundError: No such file: '/tmp/tmp2mvm8hya/mean.nii.gz'
During running the processing pipeline:
share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl -i "/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/TRT_0379/TRT_0379_asl.nii.gz" --ibf=rpt --iaf=tc --tis 3.00 --bolus 1.50 --casl --fslanat="/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/TRT_0379/brain.anat" --t1 1.30 --bat 1.30 --t1b 1.65 --alpha 0.85 --fixbolus --spatial --artoff -o "/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test"
OXFORD_ASL - running
Version: v3.9.22 Fri Jan 4 12:57:54 2019
Saving results in natve (ASL aquisition) space to /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/native_space
Saving results in structural space to /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/struct_space
Pre-processing
asl_file: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
Cannot open volume /tmp/fsl_cc6eFD_ox_asl/diffdata_mean for reading!
ERROR: Could not open file
Number of inversion times: 1
Number of timepoints in data:
expr: syntax error
Number of repeats in data:
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 1381: ((: r<: syntax error: operand expected (error token is "<")
3.00
Performing registration
ASL_REG
Input file is: /tmp/fsl_cc6eFD_ox_asl/meanasl_brain
Registration MAIN stage (FLIRT)
Tidying up
ASL_REG - Done.
Creating mask
Setting up BASIL
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 1874: [: -eq: unary operator expected
Instructing BASIL to use automated spatial smoothing
Calling BASIL on data - conventional perusion image
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 1946: [: -gt: unary operator expected
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 1946: [: -eq: unary operator expected
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 1961: [: -gt: unary operator expected
Creating output directory: /tmp/fsl_cc6eFD_ox_asl/basil
here
STEP 1: VB - Tissue
fabber_asl: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
Could not find a supported file with prefix "/tmp/fsl_cc6eFD_ox_asl/basil/step1/finalMVN"
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/basil: line 79: /tmp/fsl_cc6eFD_ox_asl/basil/step1/info.txt: No such file or directory
STEP 2: Spatial VB Tissue - init with STEP 1
fabber_asl: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
Could not find a supported file with prefix "/tmp/fsl_cc6eFD_ox_asl/basil/step2/finalMVN"
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/basil: line 74: /tmp/fsl_cc6eFD_ox_asl/basil/step2/info.txt: No such file or directory
End.
ls: cannot access /tmp/fsl_cc6eFD_ox_asl/basil/step?: No such file or directory
Cannot open volume /mean_ftiss for reading!
Cannot open volume /mean_delttiss for reading!
Fabber variance calculator
Working in -m
cat: invalid option -- 'm'
Try 'cat --help' for more information.
Done.
Cannot open volume /var_ftiss for reading!
Cannot open volume /var_delttiss for reading!
Could not find a supported file with prefix "/finalMVN"
cp: cannot stat ‘/paramnames.txt’: No such file or directory
Performing final registration
Performing registration
ASL_REG
Input file is: /tmp/fsl_cc6eFD_ox_asl/ftiss
Registration FINAL stage (BBR)
Cannot open volume /tmp/fsl_cc6eFD_ox_asl/ftiss for reading!
'/tmp/fsl_cc6eFD_ox_asl/mask.nii.gz' and '/tmp/fsl_cc6eFD_ox_asl/mask.nii.gz' are the same file
Running BBR
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_4dcyGe_asl_reg/asldata_brain
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/epi_reg: line 338: 5593 Aborted (core dumped) $FSLDIR/bin/flirt -ref ${vrefhead} -in ${vepi} -dof 6 -cost bbr -wmseg ${vout}_fast_wmseg -init ${vout}_init.mat -omat ${vout}.mat -out ${vout} -schedule ${FSLDIR}/etc/flirtsch/bbr.sch
Could not open matrix file /tmp/fsl_4dcyGe_asl_reg/low2high_final.mat
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_4dcyGe_asl_reg/asldata_brain
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/epi_reg: line 338: 5596 Aborted (core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline
BBR end
Saving FINAL output
cp: cannot stat ‘/tmp/fsl_4dcyGe_asl_reg/low2high_final.mat’: No such file or directory
Could not find a supported file with prefix "/tmp/fsl_4dcyGe_asl_reg/low2high_final"
'/tmp/fsl_cc6eFD_ox_asl/tissseg.nii.gz' and '/tmp/fsl_cc6eFD_ox_asl/tissseg.nii.gz' are the same file
Tidying up
ASL_REG - Done.
Could not find a supported file with prefix "/tmp/fsl_cc6eFD_ox_asl///ftiss"
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_cc6eFD_ox_asl///ftiss
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 174: 6174 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2struct.mat -ref $tempdir/struc -out $outdir/struct_space/$subdir/$parname $APPLYXFM_OPTS
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_cc6eFD_ox_asl///ftiss
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 174: 6186 Aborted (core dumped) applywarp --in=$tempdir/$subdir/$param --out=$outdir/std_space/$subdir/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Image Exception : #22 :: ERROR: Could not open image /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/native_space///perfusion
Cannot open volume /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/std_space///perfusion for reading!
Cannot open volume /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/native_space///perfusion for reading!
Cannot open volume /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/struct_space///perfusion for reading!
Could not find a supported file with prefix "/tmp/fsl_cc6eFD_ox_asl///delttiss"
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_cc6eFD_ox_asl///delttiss
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 174: 6246 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2struct.mat -ref $tempdir/struc -out $outdir/struct_space/$subdir/$parname $APPLYXFM_OPTS
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_cc6eFD_ox_asl///delttiss
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 174: 6299 Aborted (core dumped) applywarp --in=$tempdir/$subdir/$param --out=$outdir/std_space/$subdir/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Image Exception : #22 :: ERROR: Could not open image /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/native_space///arrival
Image Exception : #22 :: ERROR: Could not open image /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/native_space///perfusion
Image Exception : #22 :: ERROR: Could not open image /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/native_space///arrival
Could not find a supported file with prefix "/tmp/fsl_cc6eFD_ox_asl///var_ftiss"
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_cc6eFD_ox_asl///var_ftiss
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 174: 6321 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2struct.mat -ref $tempdir/struc -out $outdir/struct_space/$subdir/$parname $APPLYXFM_OPTS
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_cc6eFD_ox_asl///var_ftiss
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 174: 6371 Aborted (core dumped) applywarp --in=$tempdir/$subdir/$param --out=$outdir/std_space/$subdir/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
(standard_in) 1: syntax error
Cannot open volume /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/std_space///perfusion_var for reading!
Cannot open volume /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/native_space///perfusion_var for reading!
Cannot open volume /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/struct_space///perfusion_var for reading!
Could not find a supported file with prefix "/tmp/fsl_cc6eFD_ox_asl///var_delttiss"
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_cc6eFD_ox_asl///var_delttiss
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 174: 6415 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2struct.mat -ref $tempdir/struc -out $outdir/struct_space/$subdir/$parname $APPLYXFM_OPTS
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_cc6eFD_ox_asl///var_delttiss
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/oxford_asl/oxford_asl: line 174: 6439 Aborted (core dumped) applywarp --in=$tempdir/$subdir/$param --out=$outdir/std_space/$subdir/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Output is /share/VA_Imaging/Projects/salat/2389_TRT/dmiller/ASL/test/
OXFORD_ASL - done.
Return code: 0
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