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Hello Michael, Thank you for your answer, but if this has run fine could you explain me some of the outputs (in directories below) not defined in FSL web site. Particularly, where could I find the CBF with partial volume correction ? */native_space* : *arrival_masked.nii.gzarrival.nii.gzarrival_wm.nii.gzasl2struct.matgm_mask.nii.gzgm_roi.nii.gzmask.nii.gzperfusion_calib_masked.nii.gzperfusion_calib.nii.gzperfusion_masked.nii.gzperfusion.nii.gzperfusion_wm_calib_masked.nii.gzperfusion_wm_calib.nii.gzperfusion_wm_masked.nii.gzperfusion_wm.nii.gzpvgm_inasl.nii.gzpvwm_inasl.nii.gzwm_mask.nii.gzwm_roi.nii.gz* */struct_space* : *arrival.nii.gzarrival_wm.nii.gzperfusion_calib.nii.gzperfusion.nii.gzperfusion_wm_calib.nii.gzperfusion_wm.nii.gz* Best regards, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France 2015-02-03 17:15 GMT+01:00 Michael Chappell <[log in to unmask]>: > I think that this has run fine - the error you are getting is in the > calibration phase and this isn’t critical to what you are doing (it is a > small bug in the code that I have fixed for a future release). > > Michael > > On 2 Feb 2015, at 15:01, Matthieu Vanhoutte <[log in to unmask]> > wrote: > > Hello, > > I tried to apply what you've explain to me, and used skull-stripped > control image for calibration and registration using default BET function : > *bash oxford_asl -i diffdata -o pvc --tis 3.175 --bolus 1.650 --casl -c > control_brain -s T1Proc_BrainSegmentation0N4 --tr 4.05 --te 14 --regfrom > control_brain --pvcorr* > > However I got error message below : > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *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_brain 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_weX0Vz_asl_calib/seg_bias terminate > called after throwing an instance of 'RBD_COMMON::BaseException' Aborted > (core dumped) Cannot open volume /tmp/fsl_weX0Vz_asl_calib/biasfield for > reading! Image Exception : #22 :: ERROR: Could not open image > /tmp/fsl_weX0Vz_asl_calib/sens terminate called after throwing an instance > of 'RBD_COMMON::BaseException' Aborted (core dumped) > M0:784.06516906099871929710 ASL_calib - DONE. Number of inversion times: 1 > Number of timepoints in data: 30 Number of repeats in data: 30 3.175 3.175 > 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 > 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 > 3.175 3.175 3.175 3.175 Setting up BASIL Calling BASIL on data Creating > output directory: /tmp/fsl_RwxCAJ_ox_asl/basil Model for analysis is: > aslpvc Using bolus length: 1.650 STEP 1: VB (2 param: CBF and ^t) > ------------------ Welcome to FABBER v2.0 Logfile started: > /tmp/fsl_RwxCAJ_ox_asl/basil/step1/logfile Start time: Mon Feb 2 15:25:39 > 2015 FABBER release v2.0 Forward Model version: $Id: > fwdmodel_asl_pvc.cc,v 1.6 2013/09/03 15:08:04 chappell Exp $ Loading > mask data from '/tmp/fsl_RwxCAJ_ox_asl/mask' Loading data from > 'diffdata' here . . . . . . . . . . Saving! FABBER is all done. Duration: > 21 seconds. Logfile was: /tmp/fsl_RwxCAJ_ox_asl/basil/step1/logfile STEP 2: > VB (4 param: CBF and ^t, fwm, ^twm) - init with STEP 1 FABBER: MVNtool > Reading MVNs from /tmp/fsl_RwxCAJ_ox_asl/basil/temp Reading MVNs from > /tmp/fsl_RwxCAJ_ox_asl/basil/temp FABBER: MVNtool Reading MVNs from > /tmp/fsl_RwxCAJ_ox_asl/basil/temp Reading MVNs from > /tmp/fsl_RwxCAJ_ox_asl/basil/temp Spatial prior specification: MNMNII STEP > 2: Spatial VB (4 param: CBF and ^t, fwm, ^twm) - init with STEP 1 FABBER: > MVNtool Reading MVNs from /tmp/fsl_RwxCAJ_ox_asl/basil/temp Reading MVNs > from /tmp/fsl_RwxCAJ_ox_asl/basil/temp FABBER: MVNtool Reading MVNs from > /tmp/fsl_RwxCAJ_ox_asl/basil/temp Reading MVNs from > /tmp/fsl_RwxCAJ_ox_asl/basil/temp FABBER: MVNtool Reading MVNs from > /tmp/fsl_RwxCAJ_ox_asl/basil/temp Reading MVNs from > /tmp/fsl_RwxCAJ_ox_asl/basil/temp ------------------ Welcome to FABBER v2.0 > FABBER: MVNtool Reading MVNs from /tmp/fsl_RwxCAJ_ox_asl/basil/temp Reading > MVNs from /tmp/fsl_RwxCAJ_ox_asl/basil/temp ------------------ Welcome to > FABBER v2.0 Logfile started: /tmp/fsl_RwxCAJ_ox_asl/basil/step2/logfile > Start time: Mon Feb 2 15:26:02 2015 FABBER release v2.0 Forward Model > version: $Id: fwdmodel_asl_pvc.cc,v 1.6 2013/09/03 15:08:04 chappell > Exp $ Expanded, --param-spatial-priors=MNMNII Loading mask data from > '/tmp/fsl_RwxCAJ_ox_asl/mask' Loading data from 'diffdata' WARNING > ONCE: Not saving finalSpatialPriors.nii.gz -- too huge!! Reading MVNs from > /tmp/fsl_RwxCAJ_ox_asl/basil/temp Using initial value for all deltas: 0.5 > Reading Image prior (5): /tmp/fsl_RwxCAJ_ox_asl/pvgm_inasl Reading Image > prior (6): /tmp/fsl_RwxCAJ_ox_asl/pvwm_inasl Starting iteration 1 of 200 > Optimizing for parameter 1 SpatialPrior 1 type M : 1e-08 0 0 delta(k) = > -3, rho(k) == 1234.57 Optimizing for parameter 2 SpatialPrior 2 type N : 0 > 0 0 delta(k) = 0, rho(k) == 0 Optimizing for parameter 3 SpatialPrior 3 > type M : 1e-08 0 0 delta(k) = -3, rho(k) == 1234.57 Optimizing for > parameter 4 SpatialPrior 4 type N : 0 0 0 delta(k) = 0, rho(k) == 0 > Optimizing for parameter 5 SpatialPrior 5 type I : 0 0 0 delta(k) = 0, > rho(k) == 0 Optimizing for parameter 6 SpatialPrior 6 type I : 0 0 0 > delta(k) = 0, rho(k) == 0 WARNING ONCE: Cache is disabled to avoid memory > problems! . . . Starting iteration 200 of 200 k=1, tmp1=3.06469e+06, > tmp2=964125 k=2, tmp1=18170.3, tmp2=166.467 k=3, tmp1=1.02814e+06, > tmp2=71954.7 k=4, tmp1=18281, tmp2=31.7044 k=5, tmp1=18.2882, tmp2=6287.18 > k=6, tmp1=18.3237, tmp2=5596.33 New akmean: 0.007923 1.740853 0.029017 > 1.743141 5.062426 5.685274 Optimizing for parameter 1 SpatialPrior 1 type M > : 0.00792342 0 0 delta(k) = -3, rho(k) == 1234.57 Optimizing for > parameter 2 SpatialPrior 2 type N : 0 0 0 delta(k) = 0, rho(k) == 0 > Optimizing for parameter 3 SpatialPrior 3 type M : 0.0290174 0 0 > delta(k) = -3, rho(k) == 1234.57 Optimizing for parameter 4 SpatialPrior 4 > type N : 0 0 0 delta(k) = 0, rho(k) == 0 Optimizing for parameter 5 > SpatialPrior 5 type I : 0 0 0 delta(k) = 0, rho(k) == 0 Optimizing for > parameter 6 SpatialPrior 6 type I : 0 0 0 delta(k) = 0, rho(k) == 0 > Coefficient resels per voxel for param 1: 0.238721 (vb) or -999 (eo) > Coefficient resels per voxel for param 2: 0.0082197 (vb) or -999 (eo) > Coefficient resels per voxel for param 3: 0.0778773 (vb) or -999 (eo) > Coefficient resels per voxel for param 4: 0.00237705 (vb) or -999 (eo) > Coefficient resels per voxel for param 5: 0.00229898 (vb) or -999 (eo) > Coefficient resels per voxel for param 6: 0.000150067 (vb) or -999 (eo) > Saving! Free energy wasn't recorded, so no freeEnergy.nii.gz created. > FABBER is all done. Duration: 324 seconds. Summary of warnings (2 distinct > warnings) Issued 800 times: Cache is disabled to avoid memory problems! > Issued once: Not saving finalSpatialPriors.nii.gz -- too huge!! Logfile > was: /tmp/fsl_RwxCAJ_ox_asl/basil/step2/logfile End. Cannot open volume > pvc/native_space///deltwm for reading! Output is pvc/ OXFORD_ASL - done.* > > You can find attached to this link the files I have used with the > oxford_asl command : > http://we.tl/L4uMFTdeXB > > I've got some outputs in /native_space and struct_space, but don't know > what they mean ? : > > /native_space : > > > > > > > > > > > > > > > > > > > *arrival_masked.nii.gz arrival.nii.gz arrival_wm.nii.gz asl2struct.mat > gm_mask.nii.gz gm_roi.nii.gz mask.nii.gz perfusion_calib_masked.nii.gz > perfusion_calib.nii.gz perfusion_masked.nii.gz perfusion.nii.gz > perfusion_wm_calib_masked.nii.gz perfusion_wm_calib.nii.gz > perfusion_wm_masked.nii.gz perfusion_wm.nii.gz pvgm_inasl.nii.gz > pvwm_inasl.nii.gz wm_mask.nii.gz wm_roi.nii.gz* > > /struct_space : > > > > > > *arrival.nii.gz arrival_wm.nii.gz perfusion_calib.nii.gz perfusion.nii.gz > perfusion_wm_calib.nii.gz perfusion_wm.nii.gz* > > Could you please take a look at these and explain me the warnings and > the outputs ? > > Many thanks in advance ! > > Best regards, > > ------------------------------------- > Matthieu Vanhoutte, MSc > Research Engineer - Department of Neuroradiology > Regional University Hospital, Lille, France > > 2015-01-27 17:11 GMT+01:00 Michael Chappell <[log in to unmask] > >: > >> I think that the problem in this case is related to the mask used fro >> processing and oxford_asl was unable to create a sensible brain mask. It >> would help if you provided the control image (that is used for calibration >> and registration here) after brain extraction. My attempt using the default >> BET parameters achieved a sensible brain extraction for the control image >> and using this oxford_asl with PVC produced results. >> >> Michael >> >> >> On 27 Jan 2015, at 11:54, Matthieu Vanhoutte < >> [log in to unmask]> wrote: >> >> Hello Michael, >> >> Thank you for helping. >> >> I hope you will find quickly the solution and I am waiting impatiently >> for the newer version ! >> >> Best regards, >> >> ------------------------------------- >> Matthieu Vanhoutte, MSc >> Research Engineer - Department of Neuroradiology >> Regional University Hospital, Lille, France >> >> Le 27/01/2015 11:16, Michael Chappell a écrit : >> >> It looks like the main (non partial volume corrected version) of the CBF >> quantification has worked and something has gone wrong at the final PVC >> step. I have seen a similar problem before and I suspect it will have >> something to do with the mask or partial volume estimates created >> internally. I will try to have a look soon and get back to you - it may be >> that this has been fixed by some improvements to oxford_asl that have not >> been released yet (in which case I might be able to give you a newer >> version temporarily). >> >> Michael >> >> On 23 Jan 2015, at 16:07, Matthieu Vanhoutte < >> [log in to unmask]> wrote: >> >> Hello experts, >> >> I remembered to use "bash" before "oxford_asl" command to prevent from >> some bugs. >> >> So it went far away but still got lot of errors : >> >> OXFORD_ASL - running >>> Creating output directory >>> Saving results in natve (ASL aquisition) space to pvc2/native_space >>> Saving results in structural space to pvc2/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_7D0Jbn_asl_calib/seg_bias >>> terminate called after throwing an instance of >>> 'RBD_COMMON::BaseException' >>> Aborted (core dumped) >>> Cannot open volume /tmp/fsl_7D0Jbn_asl_calib/biasfield for reading! >>> Image Exception : #22 :: ERROR: Could not open image >>> /tmp/fsl_7D0Jbn_asl_calib/sens >>> terminate called after throwing an instance of >>> 'RBD_COMMON::BaseException' >>> Aborted (core dumped) >>> M0:785.90172355273613219438 >>> ASL_calib - DONE. >>> Number of inversion times: 1 >>> Number of timepoints in data: 30 >>> Number of repeats in data: 30 >>> 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 >>> 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 3.175 >>> 3.175 3.175 3.175 3.175 3.175 3.175 >>> Setting up BASIL >>> Calling BASIL on data >>> Creating output directory: /tmp/fsl_eIyKnR_ox_asl/basil >>> Model for analysis is: aslpvc >>> Using bolus length: 1.650 >>> STEP 1: VB (2 param: CBF and ^t) >>> ------------------ >>> Welcome to FABBER v2.0 >>> Logfile started: /tmp/fsl_eIyKnR_ox_asl/basil/step1/logfile >>> Start time: Fri Jan 23 16:52:01 2015 >>> FABBER release v2.0 >>> Forward Model version: >>> $Id: fwdmodel_asl_pvc.cc,v 1.6 2013/09/03 15:08:04 chappell Exp $ >>> Loading mask data from '/tmp/fsl_eIyKnR_ox_asl/mask' >>> Loading data from 'diffdata' >>> here >>> . . . . . . . . . . Saving! >>> FABBER is all done. >>> Duration: 90 seconds. >>> Logfile was: /tmp/fsl_eIyKnR_ox_asl/basil/step1/logfile >>> STEP 2: VB (4 param: CBF and ^t, fwm, ^twm) - init with STEP 1 >>> FABBER: MVNtool >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> FABBER: MVNtool >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> Spatial prior specification: MNMNII >>> STEP 2: Spatial VB (4 param: CBF and ^t, fwm, ^twm) - init with STEP 1 >>> FABBER: MVNtool >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> FABBER: MVNtool >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> FABBER: MVNtool >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> ------------------ >>> Welcome to FABBER v2.0 >>> FABBER: MVNtool >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> Reading MVNs from /tmp/fsl_eIyKnR_ox_asl/basil/temp >>> ------------------ >>> Welcome to FABBER v2.0 >>> Logfile started: /tmp/fsl_eIyKnR_ox_asl/basil/step2/logfile >>> Start time: Fri Jan 23 16:53:39 2015 >>> FABBER release v2.0 >>> Forward Model version: >>> $Id: fwdmodel_asl_pvc.cc,v 1.6 2013/09/03 15:08:04 chappell Exp $ >>> Expanded, --param-spatial-priors=MNMNII >>> Loading mask data from '/tmp/fsl_eIyKnR_ox_asl/mask' >>> Loading data from 'diffdata' >>> fabber: inference_spatialvb.cc:1982: void >>> SpatialVariationalBayes::CalcNeighbours(const NEWIMAGE::volume<float>&): >>> Assertion `checkNofN == 1' failed. >>> Aborted (core dumped) >>> End. >>> Cannot open volume /tmp/fsl_eIyKnR_ox_asl/basil/step2/mean_ftiss for >>> reading! >>> Cannot open volume /tmp/fsl_eIyKnR_ox_asl/basil/step2/mean_delttiss for >>> reading! >>> Cannot open volume /tmp/fsl_eIyKnR_ox_asl/basil/step2/mean_fwm for >>> reading! >>> Cannot open volume /tmp/fsl_eIyKnR_ox_asl/basil/step2/mean_deltwm for >>> reading! >>> Image Exception : #22 :: ERROR: Could not open image >>> /tmp/fsl_eIyKnR_ox_asl///ftiss >>> terminate called after throwing an instance of >>> 'RBD_COMMON::BaseException' >>> /home/global//fsl50/bin/oxford_asl: line 173: 8854 >>> Aborted (core dumped) flirt -in $tempdir/$subdir/$param >>> -applyxfm -init $tempdir/asl2struct.mat -ref $struc -out >>> $outdir/struct_space/$subdir/$parname >>> Image Exception : #22 :: ERROR: Could not open image >>> /tmp/fsl_eIyKnR_ox_asl///delttiss >>> terminate called after throwing an instance of >>> 'RBD_COMMON::BaseException' >>> /home/global//fsl50/bin/oxford_asl: line 173: 8903 >>> Aborted (core dumped) flirt -in $tempdir/$subdir/$param >>> -applyxfm -init $tempdir/asl2struct.mat -ref $struc -out >>> $outdir/struct_space/$subdir/$parname >>> Image Exception : #22 :: ERROR: Could not open image >>> /tmp/fsl_eIyKnR_ox_asl///ftisswm >>> terminate called after throwing an instance of >>> 'RBD_COMMON::BaseException' >>> /home/global//fsl50/bin/oxford_asl: line 173: 8952 >>> Aborted (core dumped) flirt -in $tempdir/$subdir/$param >>> -applyxfm -init $tempdir/asl2struct.mat -ref $struc -out >>> $outdir/struct_space/$subdir/$parname >>> Image Exception : #22 :: ERROR: Could not open image >>> /tmp/fsl_eIyKnR_ox_asl///deltwm >>> terminate called after throwing an instance of >>> 'RBD_COMMON::BaseException' >>> /home/global//fsl50/bin/oxford_asl: line 173: 9001 >>> Aborted (core dumped) flirt -in $tempdir/$subdir/$param >>> -applyxfm -init $tempdir/asl2struct.mat -ref $struc -out >>> $outdir/struct_space/$subdir/$parname >>> Cannot open volume pvc2/native_space///perfusion for reading! >>> Cannot open volume pvc2/native_space///perfusion_wm for reading! >>> Cannot open volume pvc2/native_space///arrival for reading! >>> Cannot open volume pvc2/native_space///deltwm for reading! >>> Cannot open volume pvc2/native_space///perfusion for reading! >>> Cannot open volume pvc2/struct_space///perfusion for reading! >>> Cannot open volume pvc2/native_space///perfusion_calib for reading! >>> Cannot open volume pvc2/native_space///perfusion_wm for reading! >>> Cannot open volume pvc2/struct_space///perfusion_wm for reading! >>> Cannot open volume pvc2/native_space///perfusion_wm_calib for reading! >>> Output is pvc2/ >>> OXFORD_ASL - done. >>> >> >> ==> End of this command, the output directory "native_space" is >> incomplete (no perfusion and perfusion_calib) and "struct_space" *is >> 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 >> >> 2015-01-23 16:43 GMT+01:00 Matthieu Vanhoutte < >> [log in to unmask]>: >> >>> 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 - running Creating output directory Saving results in natve >>> (ASL aquisition) space to pvc2/native_space Saving results in structural >>> space to pvc2/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_18mRY5_asl_calib/seg_bias terminate >>> 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/sens terminate called after throwing an instance >>> of 'RBD_COMMON::BaseException' Aborted (core dumped) >>> M0:785.90172355273613219438 ASL_calib - DONE. >>> /home/global//fsl50/bin/oxford_asl: 1060: >>> /home/global//fsl50/bin/oxford_asl: alltis[0]=3.175: not found Number of >>> inversion times: 1 Number of timepoints in data: 30 Number 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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> >> >> --- >> 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 >> >> >> >> >> > >