Hello,

I would like to use conn to remove WM, CSF, and motion regressors from my fMRI timeseries, to then further analyse the denoised timeseries with SPM.

I checked the box "create confound corrected time-series" and conn produced a large .nii file that contains the denoised files. However, neither SPM nor conn can work with this file. If I try to select this .nii file, there is an error saying that conn cannot view this image. I tried to split the data with fslsplit. This results in the right amount of images, right dimensions, and reasonable voxel intensities. Do you have any idea what could go wrong with reading these files?

The other question is where I can find the actual confound regressors that get removed in the end? Would it be the file ROI_Subject001_Condition001.mat? However, there are three possible locations (d1data, d2data, and data). They all have information regarding the regressors. Do you mind explaining how these are different? Or point me to a manual that explains the output of conn in such detail?

Any help would be appreciated.
Thanks,
Conny