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--region-analysis not calculated #28

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ChristianNSchmitz opened this issue Feb 27, 2023 · 3 comments
Open

--region-analysis not calculated #28

ChristianNSchmitz opened this issue Feb 27, 2023 · 3 comments

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@ChristianNSchmitz
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Dear basil-developers,

we are using oxford_asl for analysing a pCASL experiment. For this, we would perform the region analysis. However, with the recent update, --region-analysis does not give any output in the native-space directory. You can find the terminal output attached.

Thank you very much and best wishes,
Christian

Terminal output:

christian: oxford_asl -i perf/$diffASL -c perf/$M0Name --fslanat=anat/${anatName%%.*}.anat --casl --mc --wp --spatial   --tis 1.2,1.2,1.2,1.2,1.7,1.7,1.7,1.7,2.2,2.2,2.2,2.2,2.7,2.7,2.7,2.7,3.2,3.2,3.2,3.2 --iaf=diff -o perf/cbf_run-01 --bolus 1.5   --tr=4.1 --cmethod=voxel --pvcorr --fmap=fmap/$calcFMAP --fmapmagbrain=fmap/$betFMAP --fmapmag=fmap/$magFMAP --pedir=-y --echospacing=0.00061 --region-analysis
    
Number of inversion times: 20
Number of timepoints in data: 20
Number of repeats in data: 1
1.2 1.2 1.2 1.2 1.7 1.7 1.7 1.7 2.2 2.2 2.2 2.2 2.7 2.7 2.7 2.7 3.2 3.2 3.2 3.21.2

Using FSL_ANAT outputs at: anat/sub-013_ses-03_run-01_T1w.anatBias field extracted from anat/sub-013_ses-03_run-01_T1w.anat sucessfullyDefaulting to brain extracted calibration image as initial registration reference
Using brain extracted calibration image as initial registration reference
Creating WMseg for BBR registration
Performing registration
Using /tmp/fsl_do1ng011_ox_asl/calib_brain as base for inital registration
Initial registration is FLIRT only
Performing registration
ASL_REG
Input file is: /tmp/fsl_do1ng011_ox_asl/calib_brain
Registration MAIN stage (FLIRT)
Tidying up
ASL_REG - Done.
Could not find a supported file with prefix "/tmp/fsl_do1ng011_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_do1ng011_ox_asl/pwi
Creating output directory
Registration FINAL stage (BBR)
Registering fieldmap to structural
Running BBR with fieldmap
0.903325 0.997920 -0.009151 -0.063810 0.000000 0.004565 0.997420 -0.071648 0.000000 0.064301 0.071207 0.995387 0.000000 -13.480339 -3.061286 37.966916 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_do1ng011_ox_asl/asldist_warp
- Jacobian: /tmp/fsl_do1ng011_ox_asl/distcorr/jacobian
Applying warps to ASL data
- Moco: /tmp/fsl_do1ng011_ox_asl/asldata.cat
Applying warps to calibration data
- Calib->ASL: /tmp/fsl_do1ng011_ox_asl/calib2asl.mat
Number of voxels is:368640
Number of repeats in data is:1
Outputting ASL data mean at each TI
Done.
T1: 1.65
T1b: 1.65
Setting up BASIL
cASL model
Infer arterial component
Fixed bolus duration
Variable arterial arrival time
Setting prior/initial (tissue/gray matter) bolus arrival time to 0
Setting std dev of the (tissue) BAT prior to 1
Instructing BASIL to use automated spatial smoothing
BASIL options (/tmp/fsl_do1ng011_ox_asl/basil_options.txt):
----
#FABBER options created by Oxford_asl --t1=1.65 --t1b=1.65 --casl --tau=1.5 --bat=0 --batsd=1 --save-model-fit       
----
Calling BASIL on data - conventional perusion image
Main run of BASIL on ASL data
Run time basil options:
--inferart --spatial
---
Creating output directory: /tmp/fsl_do1ng011_ox_asl/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_do1ng011_ox_asl/basil/step1/logfile
100%

Final logfile: /tmp/fsl_do1ng011_ox_asl/basil/step1/logfile
STEP 2: VB - Tissue Arterial - 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_do1ng011_ox_asl/basil/step2/logfile
100%

Final logfile: /tmp/fsl_do1ng011_ox_asl/basil/step2/logfile
STEP 3: Spatial VB Tissue Arterial - init with STEP 2
----------------------
Welcome to FABBER 4.0.11-12-g99c29e6-dirty
----------------------
Last commit: Wed May 11 07:38:41 2022
Logfile started: /tmp/fsl_do1ng011_ox_asl/basil/step3/logfile
100%

Final logfile: /tmp/fsl_do1ng011_ox_asl/basil/step3/logfile
End.
Using BASIL step /tmp/fsl_do1ng011_ox_asl/basil/step3
Fabber variance calculator
Working in /tmp/fsl_do1ng011_ox_asl/basil/step3
Calculating variance for: ftiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=21
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/basil/step3/finalMVN mean value=17.1625
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/basil/step3/var_ftiss
Calculating variance for: fblood
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=21
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/basil/step3/finalMVN mean value=17.1625
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/basil/step3/var_fblood
Calculating variance for: delttiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=21
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/basil/step3/finalMVN mean value=17.1625
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/basil/step3/var_delttiss
Calculating variance for: deltblood
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=21
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/basil/step3/finalMVN mean value=17.1625
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/basil/step3/var_deltblood
Done.
Performing final registration
Performing registration
ASL_REG
Input file is: /tmp/fsl_do1ng011_ox_asl/ftiss
Registration FINAL stage (BBR)
'/tmp/fsl_do1ng011_ox_asl/mask.nii.gz' and '/tmp/fsl_do1ng011_ox_asl/mask.nii.gz' are the same file
Running BBR
0.879822 0.998553 -0.014613 -0.051762 0.000000 0.011728 0.998384 -0.055604 0.000000 0.052491 0.054916 0.997110 0.000000 -12.875685 -1.856202 36.612064 1.000000
BBR end
Saving FINAL output
'/tmp/fsl_do1ng011_ox_asl/tissseg.nii.gz' and '/tmp/fsl_do1ng011_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
WARNING: Final analysis mask contains 12 voxels that were not in original model fitting mask
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:76526
Number of repeats in data is:1
Start extrapolation!
Done.
Output: ftiss perfusion / /
Mean perfusion in gm is 3.724783
Mean perfusion in cortical gm is 4.167980
Output: delttiss arrival / /
Mean arrival in gm is 0.235311
Mean arrival in cortical gm is 0.246298
Output: fblood aCBV / /
Mean perfusion in wm is 3.020688
Mean perfusion in cerebral wm is 3.125958
Mean arrival in wm is 0.290161
Mean arrival in cerebral wm is 0.302205
Output: var_ftiss perfusion_var / /
Output: var_delttiss arrival_var / /
Output: ftiss_calib perfusion_calib / /
Mean perfusion_calib in gm is 17.081349
Mean perfusion_calib in cortical gm is 18.123759
Mean perfusion_calib in wm is 14.379765
Mean perfusion_calib in cerebral wm is 14.417690
Output: var_ftiss_calib perfusion_var_calib / /
Output: fblood_calib aCBV_calib / /
Could not find a supported file with prefix "perf/cbf_run-01/native_space/sensitivity"
Run time basil options:
--inferart --spatial --pgm /tmp/fsl_do1ng011_ox_asl/pvgm_inasl --pwm /tmp/fsl_do1ng011_ox_asl/pvwm_inasl
---
Creating output directory: /tmp/fsl_do1ng011_ox_asl/pvcorr/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_do1ng011_ox_asl/pvcorr/basil/step1/logfile
100%

Final logfile: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step1/logfile
STEP 2: VB - Tissue Arterial - 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_do1ng011_ox_asl/pvcorr/basil/step2/logfile
100%

Final logfile: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step2/logfile
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/temp'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=55
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/temp mean value=9.63145
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/temp_ftiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/temp'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=55
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/temp mean value=9.63145
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/gmcbf_init'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/gmcbf_init mean value=8.30196
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/temp
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/temp'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=55
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/temp mean value=9.70365
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/wmcbf_init'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/wmcbf_init mean value=3.32078
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/temp
STEP 3: Spatial VB Tissue Arterial PVE - init with STEP 2
----------------------
Welcome to FABBER 4.0.11-12-g99c29e6-dirty
----------------------
Last commit: Wed May 11 07:38:41 2022
Logfile started: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/logfile
100%

Final logfile: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/logfile
End.
Using BASIL step /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3
Fabber variance calculator
Working in /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3
Calculating variance for: ftiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=55
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN mean value=9.12279
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/var_ftiss
Calculating variance for: fwm
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=55
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN mean value=9.12279
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/var_fwm
Calculating variance for: fblood
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=55
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN mean value=9.12279
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/var_fblood
Calculating variance for: delttiss
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=55
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN mean value=9.12279
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/var_delttiss
Calculating variance for: deltwm
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=55
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN mean value=9.12279
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/var_deltwm
Calculating variance for: deltblood
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=55
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN mean value=9.12279
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/var_deltblood
Calculating variance for: pvgm
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=55
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN mean value=9.12279
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/var_pvgm
Calculating variance for: pvwm
FABBER: MVNtool
FabberRunDataNewimage::Loading mask data from '/tmp/fsl_do1ng011_ox_asl/mask_dil'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=1
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=1 sec
FabberRunDataNewimage::Intents: 0, 0, 0, 0
FabberRunDataNewimage::Setting coordinates from extent
FabberRunDataNewimage::Loading data from '/tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN'
FabberRunDataNewimage::Dimensions: x=96, y=96, z=40, vols=55
FabberRunDataNewimage::Voxel size: x=2.5mm, y=2.5mm, z=3mm, TR=4.22 sec
FabberRunDataNewimage::Intents: 1005, 0, 0, 0
FabberRunDataNewimage::Applying mask to data...
FabberRunDataNewimage::GetVoxelData: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/finalMVN mean value=9.12279
FabberRunDataNewimage::Saving to nifti: /tmp/fsl_do1ng011_ox_asl/pvcorr/basil/step3/var_pvwm
Done.
Output: ftiss perfusion pvcorr pvcorr
Mean perfusion in gm is 4.493814
Mean perfusion in cortical gm is 5.092240
Output: delttiss arrival pvcorr pvcorr
Mean arrival in gm is 0.269593
Mean arrival in cortical gm is 0.288026
Output: fblood aCBV pvcorr pvcorr
Output: ftisswm perfusion_wm pvcorr pvcorr
Mean perfusion_wm in wm is 4.273282
Mean perfusion_wm in cerebral wm is 4.396017
Output: deltwm arrival_wm pvcorr pvcorr
Mean arrival_wm in wm is 0.545623
Mean arrival_wm in cerebral wm is 0.553505
Output: var_ftiss perfusion_var pvcorr pvcorr
Output: var_delttiss arrival_var pvcorr pvcorr
Output: var_ftisswm perfusion_wm_var pvcorr pvcorr
Output: var_deltwm arrival_wm_var pvcorr pvcorr
Output: ftiss_calib perfusion_calib pvcorr pvcorr
Mean perfusion_calib in gm is 20.377369
Mean perfusion_calib in cortical gm is 21.988766
Output: ftisswm_calib perfusion_wm_calib pvcorr pvcorr
Mean perfusion_wm_calib in wm is 20.470155
Mean perfusion_wm_calib in cerebral wm is 20.365931
Output: var_ftiss_calib perfusion_var_calib pvcorr pvcorr
Output: var_ftisswm_calib perfusion_wm_var_calib pvcorr pvcorr
Output: fblood_calib aCBV_calib pvcorr pvcorr
unknown option --oxasl-output
usage: /home/christian/fsl/bin/python [option] ... [-c cmd | -m mod | file | -] [arg] ...
Try `python -h' for more information.
Output is perf/cbf_run-01/
OXFORD_ASL - done.
@kishore-unm
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Correct. I am facing the same issue. The --region-analysis is flag is not generating any output in the native space folder like the manual described and I am encountering the following error:
Traceback (most recent call last):
File "/usr/local/fsl/bin/oxford_asl_roi_stats", line 5, in
from oxford_asl.roi_stats import main
ModuleNotFoundError: No module named 'oxford_asl'

I wonder if anyone can help with this! Thanks.

@mcraig-ibme
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Apologies for the slow response.

I think this is a different issues to #29 . The relevant error seems to be unknown option --oxasl-output. I think this is an old issue which has been fixed in the most recent FSL release. What version of FSL are you using?

@mcraig-ibme mcraig-ibme mentioned this issue Jun 7, 2023
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@kishore-unm
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kishore-unm commented Jun 7, 2023 via email

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@mcraig-ibme @ChristianNSchmitz @kishore-unm