Hello and thanks for this toolbox!

I am using an ISSS sequence where, for each trial, stimuli are presented during a silent period (during which no data is collected) which is followed by two whole brain acquisitions. As the data is therefore not continuous I did not convolve the model with a canonical HRF. Instead I used an FIR approach where the scans are concatenated, the onset of the first scan is input into the model with two time bins, one for each scan, modeled as separate regressors (see Peelle, 2014). Therefore each condition has two regressors corresponding to the two scans which appear in the design matrix as different basis functions (e.g., Sn(1) IsoNT*bf(1) and Sn(1) IsoNT*bf(2)).  
First question: what happens with the deconvolution step if the model was never convolved with an HRF?

So far I have been able use gPPI to generate first and second level results while ignoring the basis functions and (presumably) averaging over both scans. However I would like to model each scan separately. I have tried doing this using the Contrail field (see below) without success. It generates and estimates the design but with only a single PPI regressor for each condition/task and then fails to generate contrasts with the error 'Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast ' many times and then 'PPI Contrasts were not estimated for some reason'

Second question: Am I using the Contrail field inappropriately? Is it even possible to estimate and generate contrasts for the two scans separately?

I would very much appreciate any help with this.
Thank you for your time!

P.subject = 'P16';
P.directory=pwd;
P.VOI= '/home/tomas/IGVP_SPM/MNI_Putamen_L.nii';
P.Region= 'Left_Putamen_gPPI';
P.Estimate = 1;
P.contrast= [];
P.extract= 'mean';
P.Tasks={'0', 'Iso_NT', 'Simple_NT', 'Complex_NT', 'Iso_T', 'Simple_T', 'Complex_T'};
P.Weights=[];
P.analysis='psy';
P.method='cond';
P.CompContrasts = 1;
P.equalroi = 0;
P.Weighted=0;
%P.WB = 0;
P.FLmask = 1;
P.Contrasts(1).left={'Iso_NT'};
P.Contrasts(1).Contrail.L = {'xbf^1'};
P.Contrasts(1).right={'none'};
P.Contrasts(1).STAT='T';
P.Contrasts(1).Weighted=0;
P.Contrasts(1).MinEvents=5;
P.Contrasts(1).name='Iso_NT_s1';

P.Contrasts(2).left={'Iso_NT'};
P.Contrasts(2).Contrail.L = {'xbf^2'};
P.Contrasts(2).right={'none'};
P.Contrasts(2).STAT='T';
P.Contrasts(2).Weighted=0;
P.Contrasts(2).MinEvents=5;
P.Contrasts(2).name='Iso_NT_s2';

... etc., for each task

P.outdir = './PPI_s1s2';
P.maskdir = './PPI_s1s2';
P.GroupDir = '/home/tomas/IGVP_SPM/PPI_contrasts_s1s2';