Hello,
Can you upload your input files to
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=700839B35190E48BF
so we can have a look at them?
Kind Regards
Matthew
> Hello!
>
> I am currently having trouble with processing a PNM analysis.
>
> My input command is as follows:
> /nrgpackages/tools/fsl5/bin/pnm_stage1 -i /This/was/the/Physio_log.txt -o /this/was/the/basename -s 400 --tr=0.72 --smoothcard=0.1 --resp=3 --cardiac=2 --trigger=1 -v
>
> The output error (verbose) was:
> /nrgpackages/tools/fsl5/bin/popp -i /This/was/the/Physio_log.txt -o /this/was/the/basename -s 400 --tr=0.72 --smoothcard=0.1 --resp=3 --cardiac=2 --trigger=1 -v
> Input matrix is 116441 by 3
> Checking options
> Main Processing
> Processing triggers in column 1
>
>
> An exception has been thrown
> Logic error:- detected by Newmat: index error: requested index = 0
>
> MatrixType = Rect # Rows = 0; # Cols = 1
> Trace: main.
>
> This error occurs in both pnm_stage_1 and popp. We've checked the contents of these files with both the `file` command to verify its contents are ASCII only, and in Matlab to verify that the data and number of triggers is all as expected.
>
> We have also proccessed a resting state run which did process properly unlike the one above:
> Input matrix is 326520 by 3
> Checking options
> Main Processing
> Processing triggers in column 1
> ERROR:: Problem with trigger timing
> Estimated time per trigger does not match with integer number of slices
> Time per trigger / TR = 0.00717593
> Processing resp in column 3
> Smoothing with 41
> Processing cardiac in column 2
> Cardiac threshold = 2986.07
> Mode loop: binsize = 40 maxh/totsamp = 0
> Mean Heart Beat Interval = 0.6525
>
>
> Interestingly, when we deleted the '--trigger' call, pnm_stage_1 and popp processed just fine but the peak detection were way off.
>
> Thanks!
> -Andrew Ji
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