I think that you also need to supply the —pvcorr option in your second call to oxford_asl, otherwise you are just supplying the PVE images but not asking for the correction to be done (as it is possible you would be supplying these images for another reason, such as calculating the mean perfusion within GM).
Michael
On 30 Jun 2015, at 15:20, Olga Boukrina <[log in to unmask]> wrote:
> Hello,
> I ran oxford_asl with and without partial volume correction and my results look identical. Here is the call without pv correction:
>
> fsl5.0-oxford_asl -i $datadir/$patient/$asldir/diffdata -o asl_standard_analysis --tis 1.8 --bolus 1.5 -c $datadir/$patient/$asldir/pretag_brain.nii.gz --tr 3 -s $datadir/$patient/$asldir/struct_brain.nii.gz --csf $datadir/$patient/$asldir/ventricles_asl_space.nii.gz --asl2struc $datadir/$patient/$asldir/tag_control_pairs_reg.mat --spatial
>
> then after creating grey and white matter masks,
> #gm:
> fsl5.0-applywarp --in={$datadir/$patient/$asldir/struct_brain_pve_1.nii.gz} --out={$datadir/$patient/$asldir/gm_asl_space.nii.gz} --ref={$datadir/$patient/$asldir/tag_control_pairs_brain.nii.gz} --premat={$datadir/$patient/$asldir/struc2asl.mat} --super --interp={spline} --superlevel={4}
> #wm:
> fsl5.0-applywarp --in={$datadir/$patient/$asldir/struct_brain_pve_2.nii.gz} --out={$datadir/$patient/$asldir/wm_asl_space.nii.gz} --ref={$datadir/$patient/$asldir/tag_control_pairs_brain.nii.gz} --premat={$datadir/$patient/$asldir/struc2asl.mat} --super --interp={spline} --superlevel={4}
>
> I run the same command with partial volume correction:
>
> fsl5.0-oxford_asl -i $datadir/$patient/$asldir/diffdata -o asl_pvcorr_analysis --tis 1.8 --bolus 1.5 -c $datadir/$patient/$asldir/pretag_brain.nii.gz --tr 3 -s $datadir/$patient/$asldir/struct_brain.nii.gz --csf $datadir/$patient/$asldir/ventricles_asl_space.nii.gz --asl2struc $datadir/$patient/$asldir/tag_control_pairs_reg.mat --spatial --pvgm $datadir/$patient/$asldir/gm_asl_space.nii.gz --pvwm $datadir/$patient/$asldir/wm_asl_space.nii.gz
>
> The resulting perfusion_calib.nii.gz images in the struct_space folder look identical between the first and the second analysis. It seems that the correction is not applied, or applied in the same way to both analyses. Please help in identifying the problem here.
>
> Thank you in advance,
>
> Olga
|