Greetings Dr. Alfonso (and forum members),

My apologies if the following is something quite intuitive and obvious but I am confused regarding the condition specification in Conn.

I have a block design experiment having five conditions. I have provided the onset time for each of them and also the duration (both in seconds) but the GUI shows me "extra" scans being associated with each of the condition. Elaborating: Condition 1 starts at 0th second and has a duration of 9s (TR = 3, so 3 scans). However, in the GUI, I see that the condition actually spans from scan 1 to scan 6 [screenshot attached]. This holds true for all the conditions.

Further to this, I opened the conn*/results/preprocessing/ROI_Subject*_Condition*.mat file to obtain the denoised time series from each of the ROI and note the following:

- The variable data has the entire time series (210 volumes)
- The variable conditionweights has five 210x1 values which roughly correspond to the condition variable selected. However, I notice that there are "extra" three scans or timeseries values which are non-zero. For example, Condition 3 starts at 4th scan and ends at 11th scan (8*3 = 24s). However, entries 4-14th are non-zero in the conditionweights variable (all five cell objects have the same trend). The same holds for other conditions.
- I use the following (suggested on a different thread) to reconstruct condition specific time series:

idx = find( conditionweights{1}>0 );
data_reduced = cellfun(@(x)x(idx,:), data, 'uni',0);

However, the number of time points are 55 for each ROI (the condition, spanning 8 scans occurs five times, so there should be 8*5 = 40 time points for the timeseries; (8+3extra)*5 = 55 time points)

At this point, I am not sure of what's happening to the condition specification. Why should there be an extra three scans being associated with each condition?


Many thanks in anticipation of your reply, for the wonderful toolbox, and your continued help!



Warm Regards

Pravesh