Hi, 

I am using CONN to running preprocessing for my dataset. During the step for functional realignment & unwarp, I believe the default is to align every single volume to the first volume. However, i am hoping to realign to the middle volume. Is there a way for me to specify this using the GUI or the batch script?

Thanks!
Bosi

Hi Bosi,

You are right that the default option in CONN is to realign to the first volume (and there was no easy way to change that default behaviour). I am attaching a patch that allows you to run any realignment step using the alternative realign-to-mean option (instead of the default realign-to-first option; this patch is for version 18a, simply copy the attached file to the conn distribution folder overwriting the file with the same name there). For example, to run realign&unwarp on your entire dataset using the realign-to-mean option, you may now use the batch syntax:

  conn_batch( 'Setup.preprocessing.steps', 'functional_realign&unwarp', 'Setup.preprocessing.rtm', 1);

Hope this helps
Alfonso

Originally posted by Bosi Chen: