Hello,

I have a cohort of subjects who have rsfMRI and T1 images, but their pathology prevents accurate MNI warping.

I'd like to pre-process each subject in their T1 native space, and use the confound-corrected time-series output from CONN to do further processing elsewhere. This is what I've tried thus far:

Load structural and functional images in Setup - Structural/Functional

Load SPM GM/WM/CSF segmentation masks (done previously) into Setup/ROIS

Under Options, check the "Create confound-corrected time-series check box, and select "Volume: same as structurals" under Analysis Space.

I then run Preprocessing with "preprocessing pipeline for surface-base analysis (in subject-space)", but I remove Structural Segmentation.

Once this has run, I was hoping it would allow me to access the Denoising step, where I could then specify my bandpass filtration limits and select "Done" to produce the "niftiDATA_Subjectx_Condition000.nii" files, but the Denoising tab is still in italics and is unselectable.

Are there other steps that I should be including to allow for my analysis? My goal is simply to have preprocessed counfound-correct rsfMRI data in the space of the subject T1 image.

Kind regards,
Chris