Dear Carolina,

great that you are also applying the scripts to your own data. There is an explanation on the wiki on how to use the scripts. http://www.nitrc.org/plugins/mwiki/index...


The entries for batch list are:

1. The directory where your data are: e.g., /home/carolina/my_data

2. full path to a subject list that contains 1 line per subject: e.g., /home/carolina/my_data/scripts/subjects.txt
with subject.txt looking like
sub001
sub002

3. what volume to start with: 0 if you do not want to remove volumes from the beginning of your run. Most of the time you want to remove some volumes from the beginning of the timeseries to allow for the magnetic field to stabilize. You would remove 4 or 5 volumes. In the fcon datasets we already did that so you don't have to remve extra points.

4. what volume to end with: the last volume - 1 (e.g., if you have 200 volumes, this number would be 199).

5. the number of volumes to include = (what volume to end with) - (what volume to start with) + 1; e.g., 199-0+1=200

6. the TR of your functional timeseries

You can see the number of volumes in your timeseries by using e.g., "3dinfo scan.nii.gz". 3dinfo is an AFNI command that gives you some info about your scan.

Maarten