I have several subjects (around 200) and I used uber_subject.py to do the pre-processing steps on them. In the result folder there are several files that have the mask word in their names, the names are:
first of all I would like to know the difference between these files.
And my second question is that how can I compute the union of several masks and combine them into a single mask. (I know that I should probably use 3dmask_tool but I don’t know how)
Here is what I have done so far Based on this tutorial,. I checked uber_subject.py and I found that it automatically does the following task for each subject:
3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+orig
Now I don’t know how to do these steps:
3dMean -datum short -prefix rm.mean rm.mask*.HEAD
3dcalc -a rm.mean+orig -expr ‘ispositive(a-0)’ -prefix full_mask.$subj
When I run the first command I get: 3dMean: No match..
Thank you very much for your time.