Your script should
almost work as you plan. Some minor points:
* you need to supply +tlrc or +orig on the input datasets in the
3dcalc lines
* you
mv sfnmask+tlrc into the dataset directory, but then use adolmask+tlrc, and at the end, move the latter back to the scripts directory
* you could just use "-mask ../scripts/adolmask+tlrc" as the input to
3dmaskave - that should work, and would prevent the repeated
mv-ing around of the mask file (whatever name it has)
* I personally would prefer to use something like ${subject}_rnaccant.txt as the output file, since the underscore would visually separate the subject identifier from the rest of the filename
* In 3dcalc, if the "-a" dataset is a 3D+time dataset but the "-b" dataset is just an single 3D volume, then the program automatically treats the "-b" dataset as if it had the same time axis as the "-a" dataset, and the single data value in each "-b" voxel is replicated along the time axis - this is what you need here (i.e., you don't have to make a temporary 3D+time dataset out of your TimeSerAvg datasets)
bob cox
