Hello Paul,
Thank you so much for your reply. It helped a lot. I went back to my logs and found it was giving an error previously but ignoring it. Since it was still giving a mean time series I didn't check.
I went to the logs and took the parts that I needed and created a function in my script like this:
flirt -in MASK -ref example_func -out SUBJECTMASK -applyxfm -init reg/standard2example_func.mat -datatype float
fslmaths SUBJECTMASK -thr 0.3 SUBJECTMASK
fslmaths SUBJECTMASK -bin SUBJECTMASK
fslmaths filtered_func_data -mul SUBJECTMASK TEMPTS
fslmeants -i TEMPTS -o MEAN_TS.txt -m SUBJECTMASK
to replace where I was using featquery. It uses the example_func, filtered_func_data, and standard2example_func.mat generated from the preprocessing level feat.
It seems to be working well for me
Thanks again,
Alexandra
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