Dear FSL experts,
I am working on PCASL data analysis using "Oxford_asl". I followed FSL wiki, and I have the following questions. I appreciate any advice you may provide regarding my questions bellow:
1. I followed the "Tag-control subtraction" method to get relative perfusion as follow:
#asl_file --data=pcasl --ntis=1 --iaf=tc --diff --out=diffdata --mean=diffdata_mean
Why the output images "diffdata " and "diffdata_mean " loose it's orientation. In otehr words, when I check the orientation of these images I see "???" instead of "RAS, LAS or ... etc"
2. I followed the "kinetic model inversion mode" to quantify perfusion in ml/100g/min (CBF) ) as follow:
I read TR and TE directly from the DICOMs header and I fed the numbers in milli secods
#oxford_asl -i diffdata -s ${in}/${i}/T1_brain.nii.gz -o Kinetic_model_inversion --tis 1 --te $te --tr $tr/1000 --fixbolus --artoff --fulldata --casl
Then I calibrate the data as follow:
#oxford_asl -i diffdata -o Calibration --tis 1 --te $te --tr $tr/1000 --fixbolus --artoff --casl --fulldata -c M0 --cref pcasl -s T1_brain
Kindly,
1. in the command oxford_asl can I,directly, input the raw 4D PCASL data (I mean after converting the DICOMs of PCASL into nifti, and avoid inputting the file "diffdata " from the previous step.
2. When I look into the "inversion time TI" in the DICOMs header, I can't find this pram. What can I do in the case (I have TR =8000 and TE=11). i mean how can I calculate TI?
3. Is it a correct procedure to apply "mcflirt" on 4D PCASL data then feed the output to the command "oxford_asl" instead of inputting the raw 4D PCASL data directly without correction?
I highly appreciate your great efforts and any help!
John
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