Dear Ilya,

I do not know if you already solved your problem, but we also have a
Philips scanner and found that indeed the Philips logfiles do not record
triggers from the scanner. There is one marker in the logfile (with the
number 20) that should indicate the end of the scan. However, in my
experience this marker is not very accurate.

To solve this problem we used the gx, gy, and gz columns (representing
switching of the gradients) in the logfile to create triggers. Maybe
this is helpful for your problem as well. I can provide you more details
if necessary.

Kind regards,
Petra van Houdt

-----Oorspronkelijk bericht-----
Van: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Namens
Ilya Veer
Verzonden: donderdag 13 september 2012 12:04
Aan: [log in to unmask]
Onderwerp: [FSL] Physiological noise modelling FSL 5

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

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