Hi Tamara, 

in the base it is good the check the brain mask, as it is used for all time points (it is fixed over time). 
To check alignment accuracy, you could use either brain mask or norm. It should not make a difference. It will be hard to find problems in that image (the blurriness will be difficult to see, unless you see ghost images etc).  Therefore, to really check alignment, you would need to open the all longitudinal runs on to of the base and go through them one by one (I would recommend to use norm.mgz). FreeView has a opacity slider, that I use to blend from one time point to the next (or to the base). That way you can see motion better. 
There are non-linear distortions in these images, so only if you see a clear global rotation or translation you need to worry. 

Best, Martin

On Nov 10, 2016, at 8:28 PM, Tamara Tavares <ttavare@uwo.ca> wrote:

Thank you for the clarification Martin

I have a follow-up question. When I load the base to  make sure it doesn't look blurry, should I check the norm.mgz or brainmask.mgz? Online says norm.mgz but I just want to make sure. Also, would the "blurriness" be obvious? 

Similarly, when I open the base and the longitudinal runs to see whether they align, again should I load the brainmask.mgz for these as well?

Thank you in advance for your help,
Tamara
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