Dear all, 

I'm a rookie in this field and I want to process my resting state data with your toolbox. I've some questions. 

I can run only one subject each time, right?

And finally, (I know it depends on my criteria), but any suggestion of which threshold for Z-score and head motion would you recommend in a resting state fmri data.

Thank you in advance!

Dear Juan,

Yes, when using the GUI you would process one subject at a time. Alternatively you may use .cfg files to define your different subjects data and process all of them sequentially using batch commands.

Regarding the thresholds, the default values (9 for z-score scan-to-scan global signal changes, and 2 for scan-to-scan head-motion composite changes) should work as a good starting point, but feel free to adapt these to best serve your data.

Last, if you are going to be analyzing resting state data, perhaps you might want to try the CONN toolbox (www.nitrc.org/projects/conn), which incorporates ART as part of the default preprocessing steps as well as other commonly used corrections used in functional connectivity analyses (e.g. CompCor for additional control of physiological/movement effects).

Hope this helps
Alfonso
Originally posted by Juan Gea:

Dear Juan and others,
could you give some additional information on the default values? It seems that '2' for scan-to-scan movement and '9' for global signal changes are arbitrary values. I wonder how they relate to the movement threshold (in mm) and z-threshold which are given in the output window. Personally, I'd like to use a threshold criterion of <3mm in linear movements and would like to apply this threshold as a standard to produce outlier matrices by batching. Do you have a hint how this can be implemented?
Additionally, it seems more difficult to identify a threshold criterion for maximum rotations. Is there a rule of thump to come to a reasonable threshold?
Thanks in advance!
Chris

I have similar question about this. What is the equation to calculate the "composite motion" and is there a unit to this?
I use 1.. But I have been assuming it is 1mm.