Hi,
I run pestical tool to correct for cardiac and respiration. It nearly run except that stage 5 the pipeline hung while waiting for mtlab to complete
 
Here is the output at stage 5.
 
Running Stage 5: Using first-pass IRFs, adjust for dither in cardiac peaks, then re-obtain IRFs and correct data
 
(etc...)

(etc...)
Here is when the error occured
 
Wait, script starting ...
 
It never went passed this step wothout tping CNTR-C, which produced this message:
 
COperation termintaed by user during squeeze (line 23)
 
In fit_each_physio_peak (line 111)
 vox=sqeeze(ima(cmakind(k),z:));
 
 
See attachment for more details.
 
Thanks much!
Jasmin

Hi Jasmin,

I think it may take several hours to run through this portion - it depends on how long your timeseries is and how many significantly-coupled cardiac voxels are detected, and in your case there were a lot. How long did you let it run before Ctl-C'ing it?

erik

Thanks Erik.

I think it run around 50 minutes. So I should let it run longer, correct.

Also, while I have your attention, I should remove the dummy scans for each run before running the pestica, correct?

Jasmin

Jasmin,

Yes, let it run longer! This is one of my biggest problems with PESTICA, the slowness of this second stage. You could also skip the second stage, it depends on how wide the filter is, but I don't have an objective recommendation for whether you should or not.

For the dummy scans, most scanners are setup so the acquisition is off for the first 3 seconds of scanning, so most users will see data that is already equilibrated. To check yours, open a dataset in AFNI and open the graph on a view, and see if there is a much stronger value for the first volume that gets much weaker for volume 2 and is equilibrated by volume 3 and beyond. If your scanner acquires those first volumes, then you'll have signal that is stronger on volume 1 than anywhere else. If you don't, then the signal will be flatter. When in doubt, ask a physicist or one of the AFNI people to look if the signal is equilibrated. Or please feel free to post an image of the timeseries and I would be happy to look.

Erik

Thanks much for feedback, Erik.

I collect my data and I collect the dummy scans. So yes, I  did remove the first 4 volumes. The reason I ask is because once I did remove the initial TR's I got an error message. But I will re-run again hoping that I may have just had a typo.

Thanks again for your help.
Best, Jasmin