Hi Ben,
overall your procedure is ok.
Still the interleaved comments down here.
Le 13/03/2011 2:24, Ben Becker a écrit :
> 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)?
Yes, your "run" is what SPM calls a "session" (could be a 1min or 1month
break between them).
You only need to generate the "mean image", as the header of the fMRI's
will be adjusted with the estimated realignment parameters.
> 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?
No need to do slice timing.
Better use a more flexible GLM, i.e. if timing of activation is of
interest to you, include the derivatives of the hrf.
> 3. Coregistration: Estimate
> - Data> Reference Image - Dependency: Realign: Estimate& reslice: Mean image?
Yes, reference is the "mean image" produced at the realignment step (via
dependency). And as source select the structural image.
> 4. Segment
> - GM& WM output files in native space?
> - Data – Dependency: Coreg: Estimate: Coregistered Images?
Yes, use the coregistered structural image (via dependency).
GM & WM are not very useful (except as a visual check that segmentation
worked smoothly) but the bias corrected structural image is.
> 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)?
Use 2 "Normalise: Write" modules, for the fMRI and structural image
separately.
For the fMRI use the output of the realignement step and specify your
fMRI voxel size, for example 3x3x3
For the structural image, use a better resolution like 1x1x1 and select,
by dependecy, the bias corrected image from the segmentation step.
> 6. Smooth
> - Images to smooth – Dependency: Normalise: Write Normalised Images (Subj. 1)?
Yes.
Cheers,
Chris
> Thanks in advance& kind regards,
>
> Ben
>
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