Dear ASL/FSL experts,
I am working on PCASL data analysis using the following commands (I followed wiki)
asl_file --data=pcasl.nii.gz --ntis=1 --iaf=tc --diff --out=diffdata --mean=diffdata_mean
oxford_asl -i diffdata.nii.gz -o Kinetic_model_inversion -s T1_bet.nii.gz -S $FSL_DIR/data/standard/MNI152_T1_2mm_brain.nii.gz --tis 2.5088 --te 0.011 --tr 5 --fixbolus --artoff --fulldata --casl --fulldata -c M0_OrientOK.nii.gz --spatial
These commands ran smoothly and the final output of CBF was produced in native space as well as in the structural space.... When looking into "oxford_asl" manual I see there is a flag "--S" for the standard space.
How can "oxford_asl" output final CBF images in the standard space (i.e. third folder for standard space). What the previous command needs to output CBF in standard space. I tried to include the flag "--S" but no images where generated in MNI
Thank you for any guidance
Jon
|