Hi, Pt,

One more question:

On your example script, 1) the input for "-inset" (in your example, it is "REST_in_DWI.nii.gz "). As I said before, I assume that this script can be for both rest-state fMRI and task based fMRI. With regard to the input file, I do not exactly know your meaning of the 4D data. I think it should be the output from the standardized preprocessing (i.e., the input is the same to those for the 3dDeconvolve step). We do this for each subject. Am I correct? Or it should be the output from the 3dDeconvolve step?

Since we do it one subject by one subject, we then have to extract the mean data from the whole group subjects - We can get the mean from all of the subjects. Is this method correct?

2) the input for the "-in_rois" (in your example, it is "ROI_ICMAP_GM+orig"). I assume that we can just put several ROIs together and get this file. For instance, I can get it via this way.
3dcalc -a 'TT_Daemon::amygdala' -b 'TT_Daemon::Hippocampus' .... -expr 'step(a)+2*step(b)+3*step(c)+....' -prefix ROI_ICMAP

3) the input for the mask, I can get it from the mean of all subjects.. Or we can just use NN27 or something else?
For instance, I can get it from this way.
3dmask_tool -input Sub*/*BrainMask+tlrc.HEAD \
-prefix mask_overlap.7 \
-frac 0.7

Could you correct me if I am wrong?
Thank you very much,
J



Edited 1 time(s). Last edit at 02/07/2017 04:09AM by Juan.