Dear Eric and All,

In stage 3, we need to select the proper frequency manually (I know that in batch mode its done automatically) you mentioned in the tutorial that If we don't have confidence, we can zoom larger. Actually i have no idea about these frequencies. is there anyway that we can compare our noise frequency (both cardiac and respiration) with some maps (in terms of QA). because i have no idea how these frequency should look like!

i know you said, you've never seen outside the 48-85 and 10-24 breaths or beats per min range. but i need some qa maps to be sure that my pestica estimation of these cardiac and respiration freq are fine! till now whenever i ran pestica i just hit pressed enter key!! because i had no idea!

Hi Pouya,
I think just accepting the defaults is fine, we (Jian Lin, Mark Lowe and I) are working on a study comparing 1) manually selecting vs 2) batch mode, and in a handful of studies it doesn't seem to matter, although we haven't completed this study yet.  I will post the results here, but it will likely be mid-May when we complete our analysis.
Erik

Thanks a lot :)

Hi all

On this same topic:

Can Stage 3 be automated?
In my data I rarely had to zoom in and for all 80 fMRIs the whole processing using a bash script took about a week because I had to be going back to see if Stage 3 was on, for each session and subject.

Can this step be automated so I don't have to choose the windows by hand?

Thanks in advance

Eduardo Garza

Hi Eduardo,

Sorry, that is indeed frustrating. This stage can be automated by using the "-b" flag for batch mode. Let me know if it works for you or if it keeps halting asking for your input.

Erik

Hi Erick

Thanks for the quick reply. More frustrating would be to not have PESTICA, but I'm glad there is a way to batch it.

Eduardo