Dear Tamer,

Right, sorry I forgot to mention this. After preprocessing, if your analyses are going to be in subject-space make sure to change the default "analysis mask" (found in the Setup.Options tab, which by default is defined in MNI-space) to either 'implicit mask' (automatically derived from the functional data) or to another explicit mask of your choice -which should be also in subject-space-.

Hope this helps

Alfonso

Originally posted by Tamer Gezici:

Dear Alfonso,

 

Thank you so much for your response.

 

These are the steps I used in my pipeline. I don't have a fieldmap, so I used this pipeline:

'functional_label_as_original'    'functional_realign&unwarp'    'functional_label_as_realigned'    'functional_slicetime'    'functional_art'    'functional_coregister_affine_noreslice'    'functional_label_as_subjectspace'    'functional_smooth'    'functional_label_as_smoothed'    'structural_segment'

 

However, the noise mask and the structural image don't seem to be registered properly.