Dear forum,

I am working with the conn_batch system in order to preprocess and denoise my fmri data for further analysis steps.
My preprocessing steps inherit:
- structural_segment
- functional_segment
- functional_art
- functional_coregister_affine
- functional_smooth

After the last smoothing my fmri data looks fine and ready to be denoised.
Here for I use linear detrending and denoising for the standard conpounds: wm, gw, cfs and realignment.
After that i convert the matc file to a nifti file.

However, the ouput nifti of this denoising steps is cut off by around half the brainheight in x-y-plane. The nifti cotains values, but those are equal to the "not in the brain" voxels.

No need to say, that those results are useless for any further analysis.

Can anybody comment on this kind of error? Anyone experienced the same ? Anyone knows how to fix it, since I tried a whole day and night and couldnt find the reason for this mischief....

Greetings and all the best
Daniel