Hi,
Thank you for your response. That is a massive help!
I hadn't actually paid much attention to the perfusion_calibration_var.nii.gz output image from basil. I opened up the image and there was a huge range from 0 to about 5000. When I looked this up in the basil documentation it says...
var_{paramname}.nii.gz The estimate variance image for parameter paramname.
I wonder if you have a bit more information on what is this image showing/how it's calculated? When I run a t-test from the command line, I would only need to include these images and not the perfusion_calibration.nii.gz?
In addition, I also saw that example (which you reference above) but I wasn't able to locate any information on flame from the command line. I need information about what the input and output options are as I couldn't find anything online.
For example, when I tried to type in the...
flameo --cope=perfusion_study.nii.gz --mask=${FSLDIR}/data/standard/MNI152_T1_2mm_brain_mask.nii.gz \
--dm=design.mat --tc=design.con --cs=design.grp --runmode=ols --ld=flameout
My version of ASL doesn't appear to like the --dm option.
Thanks so much for your help,
Jennifer
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