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Michael, Yes, I've seen the output. I was wondering what is the difference between absolute and relative perfusion? I need to do any other preprocessing steps before compared condition between group? thanks again for your support Davide Davide Momi ----------- PhD Candidate Unit of Behavioral Economics and Neuroeconomics Department of Neuroscience, Imaging and Clinical Sciences University "G. d'Annunzio" of Chieti Via dei Vestini 31, 66013 Chieti, Italy Mobile ++39 - 348-2650293 2018-01-17 12:04 GMT+01:00 Michael Chappell <[log in to unmask]>: > Davide, > > What do you mean by ‘pre processing’ in this context? oxford_asl should > provide all results, both relative and absolute perfusion in native_space, > along with results in structural space if appropriate. > > Michael > > On 17 Jan 2018, at 05:40, Davide Momi <[log in to unmask]> wrote: > > Thanks Michael!! Now it works well. I was wondering whether is possibile > run the pre processing in the subject space (without any normalization step) > > Best > > Davide > > On Jan 15, 2018 16:16, "Michael Chappell" <[log in to unmask]> > wrote: > >> This could well be a shell issue, you should be fine if you run it under >> a bash shell, but a few people have had issues when their terminal doesn’t >> support the use of arrays (something we have fixed in the pre-release of >> the BASIL tools). >> >> Michael >> >> >> On 12 Jan 2018, at 16:16, Davide Momi <[log in to unmask]> wrote: >> >> Hello, >> >> thanks for your reply. This is the script that I've run: >> >> oxford_asl -i /home/max/Scrivania/sb1/FUNC/PASL.nii -o >> /home/max/Scrivania/pippo/ -s /home/max/Scrivania/sb1/STRUC/T1_brain.nii.gz >> -c /home/max/Scrivania/sb1/FUNC/M0.nii --tr=3 --tis=1.8 >> >> But I still get the same error: >> >> OXFORD_ASL - running >> Saving results in natve (ASL aquisition) space to >> /home/max/Scrivania/pippo//native_space >> Saving results in structural space to /home/max/Scrivania/pippo//str >> uct_space >> Pre-processing >> Creating mask >> Performing registration >> ASL_REG >> Input file is: /tmp/fsl_3gh19b_ox_asl/meanasl >> Running FLIRT >> Tidying up >> ASL_REG - Done. >> Calculating M0a - calling ASL_CALIB >> ASL_CALIB >> Tissue reference is: csf >> M0:1410.13000000000000000000 >> ASL_calib - DONE. >> /usr/local/fsl/bin/oxford_asl: 1176: /usr/local/fsl/bin/oxford_asl: >> alltis[0]=1.8: not found >> Number of inversion times: 1 >> Number of timepoints in data: 88 >> Number of repeats in data: 88 >> >> Any tips? >> >> Davide >> >> >> >> Davide Momi >> ----------- >> PhD Candidate >> Unit of Behavioral Economics and Neuroeconomics >> Department of Neuroscience, Imaging and Clinical Sciences >> University "G. d'Annunzio" of Chieti >> <https://maps.google.com/?q=Chieti+%0D+Via+dei+Vestini+31&entry=gmail&source=g> >> Via dei Vestini 31, 66013 Chieti >> <https://maps.google.com/?q=Chieti+%0D+Via+dei+Vestini+31&entry=gmail&source=g>, >> Italy >> Mobile ++39 - 348-2650293 <+39%20348%20265%200293> >> >> 2018-01-12 16:49 GMT+01:00 Michael Chappell < >> [log in to unmask]>: >> >>> From your scan parameters you only have one TI (at least as far as >>> oxford_asl understands the term). You are clearly using pASL and your TI is >>> 1.8 (your TI2) seconds and your bolus duration is 0.7 seconds (your TI1). >>> >>> Michael >>> >>> >>> On 12 Jan 2018, at 13:28, Davide Momi <[log in to unmask]> wrote: >>> >>> Dear FSL experts, >>> >>> From previous exchanges it wasn't clear to me what is the solution to >>> this problem. The Oxford_ASL script produces an error: >>> SCRIPT LINE: oxford_asl -i data_pasl/diffdata --tis 0.7, 1.8 -o ex1_1 >>> --bolus 1.1 --bat 0.7 --t1 1.3 --t1b 1.66 --artoff --spatial >>> >>> /usr/local/fsl/bin/oxford_asl: 1176: /usr/local/fsl/bin/oxford_asl: >>> alltis [0]= 0: not found >>> /usr/local/fsl/bin/oxford_asl: 1176: /usr/local/fsl/bin/oxford_asl: >>> alltis [0]= 7: not found >>> >>> Number of inversion time: 2 >>> Number of timepoints in data: 88 >>> Number of repeats in data: 44 >>> >>> I was wondering what shall I put as TIs. I mean my machine parameters >>> are: >>> >>> - Inversion Time 1: 0.7 >>> - Saturation Stop Time: 1,6 >>> - Inversion Time 2: 1,8 >>> >>> Could you please help me with that? >>> >>> Thanks >>> >>> >>> --- >>> Michael Chappell MEng DPhil >>> W: http://www.ibme.ox.ac.uk/qubic >>> T: +44 1865 617657 <+44%201865%20617657> >>> 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.onbicdt.ox.ac.uk >>> Governing Body Fellow, Wolfson College, Oxford. >>> http://www.wolfson.ox.ac.uk >>> >>> PhysiologyforEngineers.org <http://physiologyforengineers.org/> >>> NeuroimagingPrimers.org <http://neuroimagingprimers.org/> >>> >>> >>> >>> >>> >>> >>> >>> >> >> --- >> Michael Chappell MEng DPhil >> W: http://www.ibme.ox.ac.uk/qubic >> T: +44 1865 617657 <+44%201865%20617657> >> 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.onbicdt.ox.ac.uk >> Governing Body Fellow, Wolfson College, Oxford. >> http://www.wolfson.ox.ac.uk >> >> PhysiologyforEngineers.org <http://physiologyforengineers.org/> >> NeuroimagingPrimers.org <http://neuroimagingprimers.org/> >> >> >> >> >> >> >> >> > --- > Michael Chappell MEng DPhil > W: http://www.ibme.ox.ac.uk/qubic > T: +44 1865 617657 <+44%201865%20617657> > 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.onbicdt.ox.ac.uk > Governing Body Fellow, Wolfson College, Oxford. > http://www.wolfson.ox.ac.uk > > PhysiologyforEngineers.org > NeuroimagingPrimers.org > > > > > > > >