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Hi, Do you have recorded scanner triggers? Currently the pnm requires these triggers (both GUI and command-line). They can be triggers at the start of each TR or for each slice. If you don't have triggers and _really_ trust the timing of the recordings (we've found in practice that these are often slightly out and that over the course of a whole experiment can lead to substantial shifts) then you could manufacture your own trigger trace by just copying an existing trace and setting all values to be zero except for one at the start of each TR, which should be set to one. Hope this helps. All the best, Mark On 13 Sep 2012, at 05:03, Ilya Veer <[log in to unmask]> wrote: > Dear FSL experts, > > Firstly, thanks a lot for the new FSL release, the new options seem very promising! > > At the moment I am trying to use the pnm_stage1 script to generate physiological noise regressors from our scanner (Philips) recordings of heart rate and respiration. The script runs without errors, though the graph in the html output only shows the first 15 seconds of the signal for peak detection. It does this consistently, irrespective of the length of the recordings and TR/sampling rate settings. I'm running the script on a mac. Could this be a bug? > > Also, when running PNM from the gui, it seems necessary to specify a column for scanner triggers. Should these be triggers generated at the start of each TR? If these aren't recorded, should the command line function always be used instead? > > Thanks for any help on this matter! > Ilya Veer