 |
 |
Hello experts, I update this post and still can't generate output datas from *oxford_asl* (with single delay pCASL data & PVC) : *oxford_asl -i diffdata -o pvc2 --tis 3.175 --bolus 1.650 --casl -c control -s T1Proc_BrainSegmentation0N4 --tr 4.05 --te 14 --regfrom control --pvcorr* This is the error message : *OXFORD_ASL - runningCreating output directorySaving results in natve (ASL aquisition) space to pvc2/native_spaceSaving results in structural space to pvc2/struct_spacePre-processingCreating maskPerforming registrationASL_REGInput file is: controlRunning FLIRTTidying upASL_REG - Done.Segmenting the structural imageCalculating M0a - calling ASL_CALIBASL_CALIBTissue reference is: csfImage Exception : #22 :: ERROR: Could not open image /tmp/fsl_18mRY5_asl_calib/seg_biasterminate called after throwing an instance of 'RBD_COMMON::BaseException'Aborted (core dumped)Cannot open volume /tmp/fsl_18mRY5_asl_calib/biasfield for reading!Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_18mRY5_asl_calib/sensterminate called after throwing an instance of 'RBD_COMMON::BaseException'Aborted (core dumped)M0:785.90172355273613219438ASL_calib - DONE./home/global//fsl50/bin/oxford_asl: 1060: /home/global//fsl50/bin/oxford_asl: alltis[0]=3.175: not foundNumber of inversion times: 1Number of timepoints in data: 30Number of repeats in data: 30/home/global//fsl50/bin/oxford_asl: 1074: /home/global//fsl50/bin/oxford_asl: Syntax error: Bad for loop variable* ==> End of this command, the output directories "native_space" and "struct_space" are *empty*... You can find attached to this link the files I have used with the oxford_asl command : http://we.tl/DXkTsFIQwX Could you please take a look at these and explain me why this problem happened ? Many thanks in advance ! Best regards, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France 2014-12-03 20:32 GMT+01:00 Michael Chappell <[log in to unmask]>: > That this error is internal to the software and not to do with your data. > However, it would not prevent the software from giving you perfusion images > and will not have adversely affected these images. > > Michael > > On 2 Dec 2014, at 17:16, Matthieu Vanhoutte <[log in to unmask]> > wrote: > > So what should I do ? > My data aren't good ? Or is this purely a software problem I can correct ? > (to obtain perfusion_calib and pvcorr CBF file) > > Best, > > Matthieu > > ------------------------------------- > Matthieu Vanhoutte, MSc > Research Engineer - Department of Neuroradiology > Regional University Hospital, Lille, France > > 2014-12-02 18:04 GMT+01:00 Michael Chappell <[log in to unmask] > >: > >> This appears to be a tiny bug due to a missing ‘&’ in asl_calib. However, >> my testing suggests that it will not have affected anything that comes >> after that point. >> >> Michael >> >> >> On 26 Nov 2014, at 17:26, Matthieu Vanhoutte < >> [log in to unmask]> wrote: >> >> Hello Michael, >> >> I have tried to run partial volume correction with this command : >> *bash oxford_asl -i diffdata -o pvc --tis 3.175 --bolus 1.650 --casl -c >> control -s T1Proc_BrainExtractionBrain --tr 4.05 --te 14 --regfrom control >> --pvcorr* >> >> But I've got this error message on ASL_CALIB step : >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> *OXFORD_ASL - running Creating output directory Saving results in natve >> (ASL aquisition) space to pvc/native_space Saving results in structural >> space to pvc/struct_space Pre-processing Creating mask Performing >> registration ASL_REG Input file is: control Running FLIRT Tidying up >> ASL_REG - Done. Segmenting the structural image Calculating M0a - calling >> ASL_CALIB ASL_CALIB Tissue reference is: csf Image Exception : #22 :: >> ERROR: Could not open image /tmp/fsl_3GAiyq_asl_calib/seg_bias terminate >> called after throwing an instance of 'RBD_COMMON::BaseException' Aborted >> (core dumped) Cannot open volume /tmp/fsl_3GAiyq_asl_calib/biasfield for >> reading! Image Exception : #22 :: ERROR: Could not open image >> /tmp/fsl_3GAiyq_asl_calib/sens terminate called after throwing an instance >> of 'RBD_COMMON::BaseException' Aborted (core dumped) >> M0:785.72033545478675808106 ASL_calib - DONE.* >> >> Where could it come from ? >> >> Best, >> >> ------------------------------------- >> Matthieu Vanhoutte, MSc >> Research Engineer - Department of Neuroradiology >> Regional University Hospital, Lille, France >> >> 2014-11-26 15:09 GMT+01:00 Matthieu Vanhoutte < >> [log in to unmask]>: >> >>> Hello Michael, >>> >>> Thank you very much for your quick and detailed answer. >>> >>> Concerning the partial volume correction, how to estimate PV and apply >>> PV correction : just by typing --pvcorr in the oxford_asl command ? >>> >>> What if I supply my own PV estimates : how should I use this with >>> command line ? >>> >>> Thanks again ! >>> >>> Best, >>> >>> ------------------------------------- >>> Matthieu Vanhoutte, MSc >>> Research Engineer - Department of Neuroradiology >>> Regional University Hospital, Lille, France >>> >>> 2014-11-26 14:16 GMT+01:00 Michael Chappell < >>> [log in to unmask]>: >>> >>>> CBF is computed using the ‘standard’ model for ASL, this is very nicely >>>> described in the Buxton 1998 paper. It is marginally different from the >>>> assumptions made in the recent white paper - although if you set the T1 of >>>> tissue equal to that of blood (=1.65 s) the you will get a model that is >>>> very close to those recommendations. The algorithm used to process the data >>>> according to the ASL model is the Chappell 2009 paper. By default >>>> oxford_asl uses the CSF in the calibration image (in your case control) to >>>> estimate the M0 value needed for absolute quantification, this also differs >>>> from the simple procedure in the white paper. >>>> >>>> Partial volume correction is possible using the --pvcorr command - by >>>> default oxford_asl will use FAST to segment the structural image and create >>>> the partial volume estimates You can supply your own PV estimates (these >>>> need to be at the same resolution as your ASL data) if you want. This will >>>> try to create a perfusion image of grey matter perfusion (along with a >>>> separate white matter estimate). This uses the method in the Chappell 2011 >>>> paper.In principle this method was originally designed for multi-delay >>>> data, experience suggests it will operate on single delay data like you are >>>> using (but do enter your data without having taken the mean over the >>>> individual repeats), but the separation will not be as effective. >>>> >>>> Michael >>>> >>>> References: >>>> Buxton 1998: Buxton, R. *et al.* A general kinetic model for >>>> quantitative perfusion imaging with arterial spin labeling. *Magn >>>> Reson Med* *40,* 383–396 (1998). >>>> White Paper: Alsop, D. C. *et al.* Recommended implementation of >>>> arterial spin-labeled perfusion MRI for clinical applications: A consensus >>>> of the ISMRM perfusion study group and the European consortium for ASL in >>>> dementia. *Magn Reson Med* (2014). doi:10.1002/mrm.25197 >>>> Chappell 2009: Chappell, M. A., Groves, A., Whitcher, B. & Woolrich, >>>> M. Variational Bayesian Inference for a Nonlinear Forward Model. *IEEE >>>> Transactions on Signal Processing* *57,* 223–236 (2009). >>>> Chappell 2011: Chappell, M. A. *et al.* Partial volume correction of >>>> multiple inversion time arterial spin labeling MRI data. *Magn Reson >>>> Med* *65,* 1173–1183 (2011). >>>> >>>> On 25 Nov 2014, at 13:41, Matthieu Vanhoutte < >>>> [log in to unmask]> wrote: >>>> >>>> Dear FSL's experts, >>>> >>>> 1) From my own pCASL data, I would like to compute the CBF map and >>>> according my parameters sequence I used this command : >>>> *bash oxford_asl -i diffdata -o asl --tis 3.175 --bolus 1.650 --casl -c >>>> control -s ExtractionBrain --tr 4.05 --te 14* >>>> >>>> Could you tell me the underlying used mathematical equations and the >>>> publications whose these equations came from ? >>>> >>>> 2) I saw since FSL 5.0.6 Partial Volume Correction is possible but I >>>> didn't found how to apply this ? >>>> >>>> Thank you in advance ! >>>> >>>> Best regards, >>>> >>>> ------------------------------------- >>>> Matthieu Vanhoutte, MSc >>>> Research Engineer - Department of Neuroradiology >>>> Regional University Hospital, Lille, France >>>> >>>> >>>> --- >>>> Michael Chappell MEng DPhil >>>> W: http://www.ibme.ox.ac.uk/qubic >>>> T: +44 1865 617657 >>>> Associate Professor, Institute of Biomedical Engineering, University of >>>> Oxford. >>>> http://www.ibme.ox.ac.uk >>>> Director of Training, EPSRC-MRC CDT in Biomedical Imaging >>>> http://www.onbi.ox.ac.uk >>>> Governing Body Fellow, Wolfson College, Oxford. >>>> http://www.wolfson.ox.ac.uk >>>> Research Fellow, FMRIB Centre >>>> http://www.fmrib.ox.ac.uk >>>> >>>> >>>> >>>> >>>> >>> >> >> --- >> Michael Chappell MEng DPhil >> W: http://www.ibme.ox.ac.uk/qubic >> T: +44 1865 617657 >> Associate Professor, Institute of Biomedical Engineering, University of >> Oxford. >> http://www.ibme.ox.ac.uk >> Director of Training, EPSRC-MRC CDT in Biomedical Imaging >> http://www.onbi.ox.ac.uk >> Governing Body Fellow, Wolfson College, Oxford. >> http://www.wolfson.ox.ac.uk >> Research Fellow, FMRIB Centre >> http://www.fmrib.ox.ac.uk >> >> >> >> >> > >