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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 - runningCreating output directorySaving results in natve (ASL aquisition) space to pvc/native_spaceSaving results in structural space to pvc/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_3GAiyq_asl_calib/seg_biasterminate 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/sensterminate called after throwing an instance of 'RBD_COMMON::BaseException'Aborted (core dumped)M0:785.72033545478675808106ASL_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 >> >> >> >> >> >