Hi all,
Very released to find this forum!
1. I have just started to learn UNIX and AFNI, so my questions might be very simple. I saw that Daniel Keeser has asked about 'anatomical scan you want to use' and 'resting-state scan you want to use', and these two items should be the names of raw images. But I am still a little confused. I did not see to3d in the 1_anatpreproc.sh nor 2_funcpreproc.sh, so am I supposed to do to3d first, save the data as .nii files and used the names of .nii files in those two itmes?

2. Also an additional question of AFNI, I did to3d for a scan of the functional data, after clicked 'save dataset' in GUI, and I only got one nii image. Is this correct?
3. A very general question. I saw that seperate step scripts get parameters passed from the batch script, some lines are like this:
## subject
subject=$1
## analysisdirectory/subject
dir=$2
## name of the anatomical scan
anat=$3

I just wonder how these parameters passed from batch script by $1, $2, $3 etc..


That's all so far. Thank you in advance!

Xinyuan