Tabitha,
For your analysis you will need to include the inversion efficiency in the final fslmaths step as part of the calibration. As you note oxford_asl includes the option to set the inversion efficiency for the data, but this is only used as part of the calibration. Thus, if, as you are, you do the calibration separately then the inversion efficiency value isn’t used.
Michael
> On 26 Apr 2020, at 21:57, Tabitha Manson <[log in to unmask]> wrote:
>
> Hi,
>
> I was wondering if you might be able to clarify how to account for labeling efficiency when calibrating ASL perfusion images.
>
> In my pipeline, I run oxford_asl (no calibration flag) to get an uncalibrated perfusion image.
>
> I then use asl_calib (saturation recovery mode) to fit for arterial magnetisation (from M0.txt).
>
> I've seen this step in the documentation:
>
> fslmaths [perfusion_image] -div cat [M0_text_file] -mul 6000 [absolute_CBF_output_image]
>
> However, would I also need to divide through by alpha (labeling efficiency) to account for that? Or, is it accounted for somewhere in oxford_asl or asl_calib already?
>
> my oxford_asl call is:
>
> oxford_asl -i $asl_data --ibf=rpt --iaf=diff --tis 0.50,0.90,1.30,1.70,2.10,2.50,2.90 --bolus 0.40 --casl --fslanat=$basil_dir/struc.anat --t1 1.30 --bat 1.30 --t1b 1.65 --alpha 0.85 --fixbolus --spatial --mc --infert1 --pvcorr -o $basil_dir
>
> (I specify alpha=0.85 there - but if I don't set the calib flag, does it do anything?)
>
> my asl_calib call is:
>
> asl_calib -i $basil_dir/native_space/pvcorr/perfusion.nii.gz -c $multi_TI_M0_data -s $basil_dir/struc.anat/T1_biascorr_brain.nii.gz -t $basil_dir/native_space/asl2struct.mat --mode satrecov --te 0.02054 --tis 0.5,1.7,2.9 --cgain 10 --tissref wm -m $basil_dir/native_space/wm_roi -o $basil_dir/native_space/perfusion_calib_wm_folder
>
> Thank you!
> Tabitha
>
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