Best,Thanks again !Concerning the partial volume correction, how to estimate PV and apply PV correction : just by typing --pvcorr in the oxford_asl command ?Hello Michael,Thank you very much for your quick and detailed answer.
What if I supply my own PV estimates : how should I use this with command line ?-------------------------------------
Matthieu Vanhoutte, MScResearch Engineer - Department of NeuroradiologyRegional University Hospital, Lille, France2014-11-26 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.25197Chappell 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:
Best regards,Thank you in advance !2) I saw since FSL 5.0.6 Partial Volume Correction is possible but I didn't found how to apply this ?Could you tell me the underlying used mathematical equations and the publications whose these equations came from ?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
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Matthieu Vanhoutte, MSc
Research Engineer - Department of NeuroradiologyRegional University Hospital, Lille, France
---Michael Chappell MEng DPhilAssociate Professor, Institute of Biomedical Engineering, University of Oxford.Director of Training, EPSRC-MRC CDT in Biomedical ImagingGoverning Body Fellow, Wolfson College, Oxford.Research Fellow, FMRIB Centre