BASIL-error #30
Description
Dear BASIL-developer,
we are using oxford_asl for analyzing a pASL experiment. However, we are currently facing an error that I am not able to figure out.
You can find the terminal output attached.
Thank you very much and best wishes,
Christian
Terminal output:
(base) christian@xlsserver:/data/Christian/sub-021/ses-03$ oxford_asl -i perf/sub-021_ses-03_run-01_asl -c perf/sub-021_ses-03_run-01_m0scan_flirt --fslanat=anat/sub-021_ses-03_run-01_T1w.anat --mc --wp --spatial --tis 1.99 --iaf=tc -o perf/cbf_run-01 --bolus 0.7 --tr=4.6 --cmethod=voxel --fmap=fmap/sub-021_ses-03_run-01_phasediff --fmapmagbrain=fmap/sub-021_ses-03_run-01_magnitude1_fsl-bet --fmapmag=fmap/sub-021_ses-03_run-01_magnitude1 --pedir=-y --echospacing=0.00061 --region-analysis
OXFORD_ASL - running
Version: v4.0.29-dirty Mon Feb 20 16:19:06 2023
Input file: perf/sub-021_ses-03_run-01_asl
Analysis in white paper mode
Pre-processing
Using structural images (bias corrected) from fsl_anat: anat/sub-021_ses-03_run-01_T1w.anat
Standard brain is: /usr/local/fsl/data/standard/MNI152_T1_2mm
Structural to standard transformation warp: anat/sub-021_ses-03_run-01_T1w.anat/T1_to_MNI_nonlin_coeff.nii.gz
Motion Correction
Motion correction to calibration image
Bolus duration: 0.7
Number of TIs in list: 1
TIs list: --ti1=1.99
Input ASL format is: tc
Input block format is: rpt
Number of voxels is:655360
Number of repeats in data is:4
Outputting ASL data mean at each TI
Done.
Number of inversion times: 1
Number of timepoints in data: 4
Number of repeats in data: 4
Operating in Single TI mode
1.99 1.99 1.99 1.99
1.99
Using FSL_ANAT outputs at: anat/sub-021_ses-03_run-01_T1w.anat
Bias field extracted from anat/sub-021_ses-03_run-01_T1w.anat sucessfully
Defaulting brain extracted mean ASL image as initial registration reference
Using brain extracted mean ASL image as initial registration reference
Creating WMseg for BBR registration
Performing registration
Using /tmp/fsl_vjf_kxhf_ox_asl/meanasl_brain as base for inital registration
Initial registration is FLIRT only
Performing registration
ASL_REG
Input file is: /tmp/fsl_vjf_kxhf_ox_asl/meanasl_brain
Registration MAIN stage (FLIRT)
Tidying up
ASL_REG - Done.
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/tmp_asl_reg/lowtohigh"
Generating calibration image in structural space
Creating mask
Generating dilated mask for initial BASIL runs
Distortion Correction using asl_reg
Performing registration
ASL_REG
Input file is: /tmp/fsl_vjf_kxhf_ox_asl/pwi
Creating output directory
Registration FINAL stage (BBR)
Registering fieldmap to structural
Running BBR with fieldmap
1.000113 0.997557 -0.069762 0.003601 0.000000 0.069843 0.995126 -0.069617 0.000000 0.001274 0.069699 0.997567 0.000000 -14.691910 2.985404 18.631045 1.000000
Making warp fields and applying registration to EPI series
BBR end
Saving FINAL output
Tidying up
ASL_REG - Done.
Applying combined warps to original data:
- Warp: /tmp/fsl_vjf_kxhf_ox_asl/asldist_warp
- Jacobian: /tmp/fsl_vjf_kxhf_ox_asl/distcorr/jacobian
Applying warps to ASL data - Moco: /tmp/fsl_vjf_kxhf_ox_asl/asldata.cat
Applying warps to calibration data - Calib->ASL: /tmp/fsl_vjf_kxhf_ox_asl/calib2asl.mat
Number of voxels is:655360
Number of repeats in data is:4
Outputting ASL data mean at each TI
Done.
T1: 1.65
T1b: 1.65
Setting up BASIL
pASL model
Fixed bolus duration
Variable arterial arrival time
Setting prior/initial (tissue/gray matter) bolus arrival time to 0
Single volume: informative noise prior will be used
Using SNR of 10 to set noise std dev
Runtime error (func=(main), adr=29): Square root of a negative number
Using a prior noise sd of:
Instructing BASIL to use automated spatial smoothing
BASIL options (/tmp/fsl_vjf_kxhf_ox_asl/basil_options.txt):
#FABBER options created by Oxford_asl --t1=1.65 --t1b=1.65 --tau=0.7 --bat=0 --prior-noise-stddev= --save-model-fit
Calling BASIL on data - conventional perusion image
Initial run of BASIL on data where we have avareged all repeats at each TI
Run time basil options:
--spatial
Creating output directory: /tmp/fsl_vjf_kxhf_ox_asl/init/basil
STEP 1: VB - Tissue
Welcome to FABBER 4.0.11-12-g99c29e6-dirty
Last commit: Wed May 11 07:38:41 2022
Logfile started: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step1/logfile
NEWMAT exception caught in fabber:
Invalid value given for option: = (Failed to convert to required type)
Final logfile: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step1/logfile
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/init/basil/step1/finalMVN"
STEP 2: Spatial VB Tissue - init with STEP 1
Welcome to FABBER 4.0.11-12-g99c29e6-dirty
Last commit: Wed May 11 07:38:41 2022
Logfile started: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/logfile
NEWMAT exception caught in fabber:
Invalid value given for option: = (Failed to convert to required type)
Final logfile: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/logfile
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/finalMVN"
End.
Using BASIL step /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/mean_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/mean_ftiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718723 Aborted (core dumped) fslmaths ${finalstep}/mean_ftiss -thr 0 $2/ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/mean_delttiss
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/mean_delttiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718726 Aborted (core dumped) fslmaths ${finalstep}/mean_delttiss -thr 0 $2/delttiss
Fabber variance calculator
Working in /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2
Calculating variance for: ftiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_vjf_kxhf_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=128, y=128, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=1.5mm, y=1.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
Voxel data not found: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/finalMVN (File is invalid or does not exist)
Calculating variance for: delttiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_vjf_kxhf_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=128, y=128, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=1.5mm, y=1.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
Voxel data not found: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/finalMVN (File is invalid or does not exist)
Done.
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/var_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/var_ftiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718739 Aborted (core dumped) fslmaths ${finalstep}/var_ftiss -bin -add 1 -uthr 1 -mul 1e12 -add ${finalstep}/var_ftiss $2/var_ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/var_delttiss
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/var_delttiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718741 Aborted (core dumped) fslmaths ${finalstep}/var_delttiss -bin -add 1 -uthr 1 -mul 1e12 -add ${finalstep}/var_delttiss $2/var_delttiss
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/init/basil/step2/finalMVN"
Main run of BASIL on ASL data
Run time basil options:
--spatial
Initial MVN for BASIL is: /tmp/fsl_vjf_kxhf_ox_asl/init/finalMVN
Creating output directory: /tmp/fsl_vjf_kxhf_ox_asl/basil
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/init/finalMVN"
STEP 1: VB - Tissue - init with STEP 0
Welcome to FABBER 4.0.11-12-g99c29e6-dirty
Last commit: Wed May 11 07:38:41 2022
Logfile started: /tmp/fsl_vjf_kxhf_ox_asl/basil/step1/logfile
NEWMAT exception caught in fabber:
Invalid value given for option: = (Failed to convert to required type)
Final logfile: /tmp/fsl_vjf_kxhf_ox_asl/basil/step1/logfile
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/basil/step1/finalMVN"
STEP 2: Spatial VB Tissue - init with STEP 1
Welcome to FABBER 4.0.11-12-g99c29e6-dirty
Last commit: Wed May 11 07:38:41 2022
Logfile started: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/logfile
NEWMAT exception caught in fabber:
Invalid value given for option: = (Failed to convert to required type)
Final logfile: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/logfile
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/basil/step2/finalMVN"
End.
Using BASIL step /tmp/fsl_vjf_kxhf_ox_asl/basil/step2
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/mean_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/mean_ftiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718791 Aborted (core dumped) fslmaths ${finalstep}/mean_ftiss -thr 0 $2/ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/mean_delttiss
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/mean_delttiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718793 Aborted (core dumped) fslmaths ${finalstep}/mean_delttiss -thr 0 $2/delttiss
Fabber variance calculator
Working in /tmp/fsl_vjf_kxhf_ox_asl/basil/step2
Calculating variance for: ftiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_vjf_kxhf_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=128, y=128, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=1.5mm, y=1.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
Voxel data not found: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/finalMVN (File is invalid or does not exist)
Calculating variance for: delttiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_vjf_kxhf_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=128, y=128, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=1.5mm, y=1.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
Voxel data not found: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/finalMVN (File is invalid or does not exist)
Done.
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/var_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/var_ftiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718805 Aborted (core dumped) fslmaths ${finalstep}/var_ftiss -bin -add 1 -uthr 1 -mul 1e12 -add ${finalstep}/var_ftiss $2/var_ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/var_delttiss
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_vjf_kxhf_ox_asl/basil/step2/var_delttiss
/usr/local/fsl/bin/oxford_asl: line 532: 1718807 Aborted (core dumped) fslmaths ${finalstep}/var_delttiss -bin -add 1 -uthr 1 -mul 1e12 -add ${finalstep}/var_delttiss $2/var_delttiss
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl/basil/step2/finalMVN"
Performing final registration
Performing registration
ASL_REG
Input file is: /tmp/fsl_vjf_kxhf_ox_asl/ftiss
Registration FINAL stage (BBR)
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl/ftiss
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_vjf_kxhf_ox_asl/ftiss
Aborted (core dumped)
'/tmp/fsl_vjf_kxhf_ox_asl/mask.nii.gz' and '/tmp/fsl_vjf_kxhf_ox_asl/mask.nii.gz' are the same file
Running BBR
Image Exception : #63 :: No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Image Exception : #22 :: Failed to read volume /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Error : No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Failed to read volume /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Error : No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Could not open matrix file /tmp/fsl_llo_qz1e_asl_reg/low2high_final.mat
Image Exception : #63 :: No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Image Exception : #22 :: Failed to read volume /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Error : No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
Error : No image files match: /tmp/fsl_llo_qz1e_asl_reg/asldata_brain
/usr/local/fsl/bin/epi_reg: line 390: 1718967 Aborted (core dumped)
BBR end
Saving FINAL output
cp: cannot stat '/tmp/fsl_llo_qz1e_asl_reg/low2high_final.mat': No such file or directory
Could not find a supported file with prefix "/tmp/fsl_llo_qz1e_asl_reg/low2high_final"
'/tmp/fsl_vjf_kxhf_ox_asl/tissseg.nii.gz' and '/tmp/fsl_vjf_kxhf_ox_asl/tissseg.nii.gz' are the same file
Tidying up
ASL_REG - Done.
Generating calibration image in structural space
Generating analysis mask from final structural registration
Using user-supplied structural->standard space warp to generate cortical GM/WM masks
T1t (for calibration): 1.3
Doing calibration using voxelwise M0 map
mkdir: cannot create directory 'perf/cbf_run-01/calib': File exists
Correcting the calibration (M0) image for short TR (using T1 of tissue 1.3)
Number of voxels is:216468
Number of repeats in data is:1
Start extrapolation!
Done.
Output: ftiss perfusion / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///ftiss"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
/usr/local/fsl/bin/oxford_asl: line 268: 1722736 Aborted (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Mean perfusion in gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Mean perfusion in cortical gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/std_space///perfusion
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: perf/cbf_run-01/std_space///perfusion
/usr/local/fsl/bin/oxford_asl: line 354: 1722741 Aborted (core dumped) fslmaths $outdir/std_space/$subdir_out/$parname -div $normval $outdir/std_space/$subdir_out/${parname}_norm
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: perf/cbf_run-01/native_space///perfusion
/usr/local/fsl/bin/oxford_asl: line 354: 1722744 Aborted (core dumped) fslmaths $outdir/native_space/$subdir_out/$parname -div $normval $outdir/native_space/$subdir_out/${parname}_norm
Image Exception : #63 :: No image files match: perf/cbf_run-01/struct_space///perfusion
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: perf/cbf_run-01/struct_space///perfusion
/usr/local/fsl/bin/oxford_asl: line 354: 1722746 Aborted (core dumped) fslmaths $outdir/struct_space/$subdir_out/$parname -div $normval $outdir/struct_space/$subdir_out/${parname}_norm
Output: delttiss arrival / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///delttiss"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///delttiss
/usr/local/fsl/bin/oxford_asl: line 268: 1722752 Aborted (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///arrival
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Mean arrival in gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///arrival
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Mean arrival in cortical gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Mean perfusion in wm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Failed to read volume perf/cbf_run-01/native_space///perfusion
Error : No image files match: perf/cbf_run-01/native_space///perfusion
Mean perfusion in cerebral wm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///arrival
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Mean arrival in wm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///arrival
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Failed to read volume perf/cbf_run-01/native_space///arrival
Error : No image files match: perf/cbf_run-01/native_space///arrival
Mean arrival in cerebral wm is
Output: var_ftiss perfusion_var / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///var_ftiss"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
/usr/local/fsl/bin/oxford_asl: line 268: 1722769 Aborted (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
(standard_in) 1: syntax error
Image Exception : #63 :: No image files match: perf/cbf_run-01/std_space///perfusion_var
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: perf/cbf_run-01/std_space///perfusion_var
/usr/local/fsl/bin/oxford_asl: line 378: 1722775 Aborted (core dumped) fslmaths $outdir/std_space/$subdir_out/${parname}_var -div $normval $outdir/std_space/$subdir_out/${parname}_var_norm
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion_var
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: perf/cbf_run-01/native_space///perfusion_var
/usr/local/fsl/bin/oxford_asl: line 378: 1722777 Aborted (core dumped) fslmaths $outdir/native_space/$subdir_out/${parname}_var -div $normval $outdir/native_space/$subdir_out/${parname}_var_norm
Image Exception : #63 :: No image files match: perf/cbf_run-01/struct_space///perfusion_var
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: perf/cbf_run-01/struct_space///perfusion_var
/usr/local/fsl/bin/oxford_asl: line 378: 1722779 Aborted (core dumped) fslmaths $outdir/struct_space/$subdir_out/${parname}_var -div $normval $outdir/struct_space/$subdir_out/${parname}_var_norm
Output: var_delttiss arrival_var / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///var_delttiss"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_delttiss
/usr/local/fsl/bin/oxford_asl: line 268: 1722790 Aborted (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss
/usr/local/fsl/bin/oxford_asl: line 313: 1722794 Aborted (core dumped) fslmaths $tempdir/$subdir_in/$param -div $Moval -mul $multiplier $tempdir/$subdir_in/${param}_calib
Output: ftiss_calib perfusion_calib / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///ftiss_calib
/usr/local/fsl/bin/oxford_asl: line 268: 1722801 Aborted (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion_calib
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Mean perfusion_calib in gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion_calib
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Mean perfusion_calib in cortical gm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion_calib
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Mean perfusion_calib in wm is
Image Exception : #63 :: No image files match: perf/cbf_run-01/native_space///perfusion_calib
Image Exception : #22 :: Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Failed to read volume perf/cbf_run-01/native_space///perfusion_calib
Error : No image files match: perf/cbf_run-01/native_space///perfusion_calib
Mean perfusion_calib in cerebral wm is
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss
/usr/local/fsl/bin/oxford_asl: line 313: 1722808 Aborted (core dumped) fslmaths $tempdir/$subdir_in/$param -div $Moval -mul $multiplier $tempdir/$subdir_in/${param}_calib
Output: var_ftiss_calib perfusion_var_calib / /
Could not find a supported file with prefix "/tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib"
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Image Exception : #63 :: No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Image Exception : #22 :: Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
Error : No image files match: /tmp/fsl_vjf_kxhf_ox_asl///var_ftiss_calib
/usr/local/fsl/bin/oxford_asl: line 268: 1722814 Aborted (core dumped) applywarp --in=$tempdir/$subdir_in/$param --out=$outdir/std_space/$subdir_out/$parname --ref=$std --premat=$tempdir/asl2struct.mat --warp=$warp $APPLYWARP_OPTS
Regionwise analysis
- Using oxford_asl output in perf/cbf_run-01/native_space
Traceback (most recent call last):
File "/usr/local/fsl/bin/oxford_asl_roi_stats", line 10, in
sys.exit(main())
File "/usr/local/fsl/lib/python3.10/site-packages/oxford_asl/roi_stats.py", line 594, in main
asl_ref = Image(os.path.join(outdir, "perfusion"))
File "/usr/local/fsl/lib/python3.10/site-packages/fsl/data/image.py", line 1246, in init
image = op.abspath(addExt(image))
File "/usr/local/fsl/lib/python3.10/site-packages/fsl/data/image.py", line 1951, in addExt
raise e
File "/usr/local/fsl/lib/python3.10/site-packages/fsl/data/image.py", line 1938, in addExt
return fslpath.addExt(prefix,
File "/usr/local/fsl/lib/python3.10/site-packages/fsl/utils/path.py", line 196, in addExt
raise PathError('Could not find a supported file '
fsl.utils.path.PathError: Could not find a supported file with prefix "perf/cbf_run-01/native_space/perfusion"
Output is perf/cbf_run-01/
OXFORD_ASL - done.