Hi, a quick question – in selecting files for analysis I've been taking the raw images prior to realignment, normalization etc.  I just wanted to confirm this is correct?  Thanks!

I believe you have to pre-processors the image prior to using ART. It asks for the rp_functional.txt that contains the motion parameters to display out liers

When you run art within matlab, in the GUI do you select the raw functional images, or do you select the realigned functional images, and why

Originally posted by Sreekrishna Ramakrishnapillai:

I was also wondering the same thing.

As the input file, do we use the realigned functionnal images? The warped images? Or the smoothed images?

I normally use the realigned, smoothed and warped images from SPM. As far I understand the toolbox just displays the outliers based on the threshold  parameters that you set. The motion parameters need to be estimated in prior by SPM and the output (rp_functional.txt) needs to be given as input. Correct me if I am wrong.

Update: i just found something from old posts:

Sep 1, 2014 05:09 AM
Alfonso Nieto-Castanon
McGovern Institute for Brain Research. MIT
RE: What do I do with the output?
Hi Ivan,
Typically you would input the images after spatial realignment and coregistration/normalization (but before spatial smoothing)
Best
Alfonso

Ha.  I wonder what the rationale is for this choice.

I would think the goal is to estimate the artifact in the data before pre-processing, and so all labs I've been in have only ever input the raw images before any preprocessing.