Hi, I'm trying to use the latest oxford_asl v4.0.3 downloaded from github, but so far have been unsuccessful to get it to run on the multiTI pCASL example data. Here's the command I used:
./oxford_asl.in -i ../multiPLDpcASL/asltc -o ../oxasl --casl --iaf=tc --tis=1.65,1.9,2.15,2.4,2.65,2.9 --bolus=1.4 --fixbolus --artoff --spatial --mc -c ../singlePLDpcASL/aslcalib --tr 4.8 --cmethod=single --csf=../multiPLDpcASL/csfmask --cblip=../singlePLDpcASL/aslcalib_PA --pedir=y --echospacing=0.00095
It seems to get through FABBER alright, but then runs into problems during Bayesian inference:
Bayesian Inference for Arterial Spin Labelling MRI
Version (build 5010)
Usage (optional parameters in {}):
-i : specify input/data file
{-o} : specify output directory
-m : specify brain mask file
-@ : specify parameter options file
{--model} : model used for analysis {default: buxton}
Extended options:
--nlls : Do least squares analysis as first step
--infertau : Add step to infer on bolus length
--infert1 : Add step to include uncertainty in T1 values
--inferart : Add step to infer on arterial compartment
--spatial : Add step that implements adaptive spatial smoothing on CBF
--fast : Do analysis in single step (appropriate for use with --spatial)
Special options:
--t1im : voxelwise T1 (tissue) estimates
Partial volume correction / CBF estimation
(enforces --spatial)
--pgm : Gray matter PV map
--pwm : White matter PV map
Error! Unrecognised option on command line: --init
ls: cannot access /tmp/fsl_PzblCo_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!
cp: cannot stat ‘/paramnames.txt’: No such file or directory
Calculating M0a - calling ASL_CALIB
ASL_CALIB
Tissue reference is: csf
WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
M0:1275.05000000000000000000
ASL_calib - DONE.
Cannot open volume /tmp/fsl_PzblCo_ox_asl///ftiss for reading!
Cannot open volume /tmp/fsl_PzblCo_ox_asl///var_ftiss for reading!
Output is ../oxasl/
OXFORD_ASL - done.
In my output folder, I only have logfile, M0.txt and refmask in the calib folder, and mask in the native_space folder. Has anyone encountered similar problems?
Thanks,
Jennie
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