I am using 3dmaskdump -o out.txt -quiet all_runs.a+orig.HEAD to extract the time series for each voxel. The procedure works fine and it generates a very large file. But I’m almost sure that non-brain parts are also included in this file, Because each picture has the dimension 64*64 and I have 48 slices. 3dmaskdump also extract time series for 196608 voxels.
Is there a way to exclude the non-brain parts?
I have several subjects and I want the exact number of voxels for each subjects, so if you are suggesting that I should use a mask, will this mask generate the same number of voxels for each subject?
Use -mask to apply a mask. Please see
the -help output for details.