Dear Janek,
Two comments about your preprocessing pipeline:
* In Realign: E&R, you can set Resliced Images to Mean image only.
* In Coregister: E, you probably want t1 to be the reference and the
functional mean to be the source (or if you want to keep using the other
way round, leave Other images as empty).
There are some examples of preprocessing batches available in SPM: click
on File: Load Batch and go to the folder spm12/batches, select for
example preproc_fmri.m and answer the few questions about slice timing
correction and number of sessions.
Best regards,
Guillaume.
On 16/11/17 16:47, Jan Stasiński wrote:
> HI guys,
>
> My apologies for reposting.
>
> I am struggling with choosing proper way to preprocess my functional and
> structural data in spm12. I have a block design with 4 runs (sessions
> per subject). And since I am planning on running 2nd level ROI analysis
> i need to coregister all the images to MNI space
>
> I would really appreciate your help in understanding which input should
> be used in this situation and whether what I am doing is actually correct.
> I have created a batch for each subject:
>
> STEP INPUT
> 1.Realign: E&R runs added as sessions
> 2.Coregister: E functional mean used as reference, t1
> used as source, all resliced functional images used as other
> 3. Segment t1 as the only volume
> 4. Normalize: W – functional forward deformation field + plus
> resliced images from all my runs
> 5. Normalize: W – structural bias corrected t1 from segment
> 6. Smooth normalized images from step 4.
>
> Questions:
> Is this batch correct?
> Should I or can I use coregistered images from step 2 instead of
> resliced images during normalization step (4)? What happens if I do?
> (visually, after checking registration there is no difference)
> Is there any way I can improve this batch?
>
> Again all help will be appreciated!
> Kind regards
> Janek
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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