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* 100 volumes collected. There were actually 101 volumes collected - I believe the 1st volume is supposed to be an M0, but it looks identical to the other volumes so I am discarding it.
Output is as follows:
mkdir /ASL/newFSL3
mkdir /ASL/newFSL3/native_space
2
/usr/local/fsl/bin/asl_file --data=/ASL/ASL1.nii --out=/ASL/newFSL3/native_space/diffData --obf=rpt --ntis=2 --ibf=rpt --iaf=tc --diff
/usr/local/fsl/bin/asl_file --data=/ASL/ASL1.nii --out=/ASL/newFSL3/native_space/diffData --obf=rpt --ntis=2 --ibf=rpt --iaf=tc --diff
Number of voxels is:57344
Number of repeats in data is:25
Done.
/usr/local/fsl/bin/bet /ASL/T1.nii /ASL/newFSL3/structural_brain
/usr/local/fsl/bin/asl_file --data=/ASL/ASL1.nii --ntis=2 --iaf=tc --spairs --out=/ASL/newFSL3/asldata_mc
Number of voxels is:57344
Number of repeats in data is:25
Dealing with odd members of pairs
Dealing with even members of pairs
Done.
/usr/local/fsl/bin/bet /ASL/newFSL3/asldata_mc_even /ASL/newFSL3/asldata_mc_even_brain
/usr/local/fsl/bin/oxford_asl -i /ASL/newFSL3/native_space/diffData -o /ASL/newFSL3 --tis 0.7,1.8 --bolus 1 --bat 0.7 --t1 1.3 --t1b 1.6 --alpha 0.98 --artoff --fixbolus -s /ASL/newFSL3/structural_brain --regfrom /ASL/newFSL3/asldata_mc_even_brain
/usr/local/fsl/bin/oxford_asl -i /ASL/newFSL3/native_space/diffData -o /ASL/newFSL3 --tis 0.7,1.8 --bolus 1 --bat 0.7 --t1 1.3 --t1b 1.6 --alpha 0.98 --artoff --fixbolus -s /ASL/newFSL3/structural_brain --regfrom /ASL/newFSL3/asldata_mc_even_brain
OXFORD_ASL - running
Saving results in structural space to /ASL/newFSL3/struct_space
Pre-processing
Creating mask
Performing registration
ASL_REG
Input file is: /ASL/newFSL3/asldata_mc_even_brain
Running FLIRT
Tidying up
ASL_REG - Done.
Number of inversion times: 2
Number of timepoints in data: 50
Number of repeats in data: 25
0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8 0.7 1.8
Number of voxels is:57344
Number of repeats in data is:25
Outputting ASL data mean at each TI
Done.
Setting up BASIL
Calling BASIL on data
Creating output directory: /tmp/fsl_7GVzfr_ox_asl/basil
Model for analysis is: buxton
Using bolus length: 1
STEP 1: VB (2 param: CBF and ^t)
------------------
Welcome to FABBER v2.0
Logfile started: /tmp/fsl_7GVzfr_ox_asl/basil/step1/logfile
Start time: Thu Mar 26 13:09:12 2015
FABBER release v2.0
Forward Model version:
$Id: fwdmodel_asl_grase.cc,v 1.22 2013/09/04 15:13:00 chappell Exp $
Loading mask data from '/tmp/fsl_7GVzfr_ox_asl/mask'
Loading data from '/tmp/fsl_7GVzfr_ox_asl/data'
here
. . . . . . . . . . Saving!
FABBER is all done.
Duration: 21 seconds.
Logfile was: /tmp/fsl_7GVzfr_ox_asl/basil/step1/logfile
End.
Output is /ASL/newFSL3/
OXFORD_ASL - done.
/usr/local/fsl/bin/asl_calib -i /ASL/newFSL3/native_space/perfusion --tissref csf --t1r 4.3 --t2r 0.75 --t2b 0.15 --te 0.0 -o /ASL/newFSL3/calibration -s /ASL/newFSL3/structural_brain -t /ASL/newFSL3/native_space/asl2struct.mat -c /ASL/newFSL3/asldata_mc_even --mode longtr --tr 3.2 --cgain 1.0
/usr/local/fsl/bin/asl_calib -i /ASL/newFSL3/native_space/perfusion --tissref csf --t1r 4.3 --t2r 0.75 --t2b 0.15 --te 0.0 -o /ASL/newFSL3/calibration -s /ASL/newFSL3/structural_brain -t /ASL/newFSL3/native_space/asl2struct.mat -c /ASL/newFSL3/asldata_mc_even --mode longtr --tr 3.2 --cgain 1.0
ASL_CALIB
Input file is: /ASL/newFSL3/native_space/perfusion
Tissue reference is: csf
M0:1617.68000000000000000000
ASL_calib - DONE.
And here are the resulting perfusion & arrival images + histograms in mricron:
(perfusion_calibrated in native space looks similar)
It really doesn't look right to me, especially when compared to the FSL example data.
Could anyone help me with what might be wrong?
Thanks very much :)