I am saving the denoised data to a NIFTI file.  I have two conditions acquired during two separate sessions.  Each fMRI data set has 190 volumes. 
I found the data in the folder conn/results/preprocessing.  The files in this directory are


BETA_denoising_Subject001.nii
DATA_Subject001_Condition000.matc
DATA_Subject001_Condition001.mat
DATA_Subject001_Condition002.mat
_list_BETA_denoising.mat
_list_BETA_denoising.txt
_list_conditions.mat
niftiDATA_Subject001_Condition000.nii
ROI_Subject001_Condition000.mat
ROI_Subject001_Condition001.mat
ROI_Subject001_Condition002.mat
vvPCeig_Subject001_Condition001.log
vvPCeig_Subject001_Condition001.mat
vvPCeig_Subject001_Condition002.log
vvPCeig_Subject001_Condition002.mat
vvPC_Subject001_Condition001.mat
vvPC_Subject001_Condition001.matc
vvPC_Subject001_Condition002.mat
vvPC_Subject001_Condition002.matc

You can see that there are three conditions located in the directory  (Conditions000, Conditions001, and Conditions002).  
The only nifti files located in this directory are

BETA_denoising_Subject001.nii
niftiDATA_Subject001_Condition000.nii

The niftiData_Subject000_Condition000.nii contains 380 volumes (=2*190).  I would like to confirm that the denoised data for both conditions have been concatenated together and are stored in this file.

If this is the case, I would also like to know is there a reason why the two separate denoised runs were concatenated together.  

Thanks

Bob