Dear SPMers,
I’d like to preprocess my fMRI event related data according to the example data set in the spm8 manual (face fmri data / chapter 29). To fasten up the analysis I want to batch the preprocessing steps. Before running the batch I’d like to hear your opinion on some issues.
My data:
2 runs of event related data (the same paradigm acquired twice, with a break of 1 minute, subjects stayed in the scanner)
T1 structural image
My preprocessing steps & my questions:
1. Realignment: Estimate & Reslice
- Realign the 2 runs together (2 runs = 2 sessions)?
2. Slice timing
- Correct the 2 runs in separate slice timing procedures or correct the 2 runs together (2 runs = 2 sessions)?
- Data > session - Dependency: Estimate & reslice: resliced images?
3. Coregistration: Estimate
- Data > Reference Image - Dependency: Realign: Estimate & reslice: Mean image?
4. Segment
- GM & WM output files in native space?
- Data – Dependency: Coreg: Estimate: Coregistered Images?
5. Normalise: Write
- Data > Subject > Parameter file – Dependency: Segment: Norm Params Subj -> MNI?
- Data > Subject > Images to write – Dependency: Slice timing Corr. Images (if slice timing for the two runs is separated in two
separate slice timing procedures: select output from both)?
6. Smooth
- Images to smooth – Dependency: Normalise: Write Normalised Images (Subj. 1)?
Thanks in advance & kind regards,
Ben
|