Hello,
Because I had trouble with skull-stripping with my raw T1 images (some skull often left in the posterior aspect of the brain), I decided to use the brainmask.mgz from Freesurfer which was properly skull-stripped. By using the brainmask, I also allowed Conn to import the segmentation files from Freesurfer. I then ran a modified version of the second volume-based preprocessing pipeline in Conn (see attached image): in brief, I just removed the "functional Creation of voxel-displacement map (VDM) for distortion correction" and replaced the realignment step with "functional Realignment & unwarp (subject motion estimation and correction)", effectively getting rid of the distortion correction part.

My questions are:
1. Since I used the brainmask.mgz which is already skull-stripped, will the skull-stripping part of the "functional Indirect Segmentation & Normalization" step have altered the image too much with the second skull-stripping step? So that I lose GM or CSF information for instance?

2. From what I understand, the "functional Indirect Segmentation & Normalization" step also resegment the Grey/White/CSF and overwrite those from Freesurfer. Is that true?

3. I want to co-register functional and structural volumes and then normalize to MNI while also keeping (and normalizing) the Grey/White/CSF segmentation from Freesurfer. If instead of the step "functional Indirect Segmentation & Normalization" I use the step "functional Indirect Normalization" (which also coregister structural and functional), will it also normalize the Grey/White/CSF segmentation from Freesurfer?
- I am asking this question because the "functional Indirect Segmentation & Normalization" step gives as output the skull-stripped normalized structural volume, normalized Grey/White/CSF masks and normalized functional volumes (all in MNI space) whereas the "functional Indirect Normalization" step gives the same thing (also seems to skull-strips; normal?) less the normalized Grey/White/CSF masks. 

4. Finally, if the answer to question #1 is that the second skull-stripping is problematic. Can I replace the step "functional Indirect Segmentation & Normalization" which skull-strips with the "functional Direct Coregistration to structural without reslicing" and subsequently "functional Direct Normalization" which do not seem to skull-strip again. How should I arrange the steps in the sequence in this case? Also in this case, how could I make sure that the Grey/White/CSF masks from Freesurfer get normalized to MNI?

Thank you and sorry for the long post,
Olivier