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Hi John,

Thanks again for your help and sorry for all the emails. The flow fields
that 'Normalise to MNI' asks for are the individual subjects' flow fields
'u_c1*.nii which look like the 3rd image selected in the attached picture.
Also included in this picture are a template, and subject's functional scan
after the 'normalise to MNI' step.

Thank you,
Simon


On Thu, Feb 24, 2011 at 12:28 PM, John Ashburner <[log in to unmask]>wrote:

> The flow field looks pretty OK to me.  I thought that you were
> referring to something that was uniformly grey.  This is the x
> component.  The other components can be viewed by looking at
> u_rc1*_Template.nii,2 and u_rc1*_Template.nii,3 (by changing the 1 in
> the file selector to 1:3).
>
> Also note that the main objective of Dartel is to align all the scans
> in the study together.  When you normalise to MNI space, the images
> that are closely aligned within study are all affine transformed to
> MNI space.  The version of MNI space is only really defined for affine
> aligned brain images (ie the rather blurred averages).  You should
> note that the single subject brain that people often overlay their
> results on does not define MNI space.  It is just the scan of a single
> individual that has been affine registered to MNI space.
>
> Best regards,
> -John
>
> On 24 February 2011 16:27, simon vandekar <[log in to unmask]> wrote:
> > Thanks for the reply John,
> >
> > As far as I can tell the template*.nii files look good, they are gray
> matter
> > images. There is also a u_rc1*_Template.nii in the same folder as my
> > template*.nii files, I've attached the image for that. Is that what my
> flow
> > fields are suppose to look like?
> >
> > Thank you,
> > Simon
> >
> > On Thu, Feb 24, 2011 at 10:47 AM, John Ashburner <[log in to unmask]>
> > wrote:
> >>
> >> It is a bit suspicious if all the u_*.nii are just zero.  I'm not sure
> >> why this would be the case.  Do the template*.nii files seem to be OK?
> >>
> >> Best regards,
> >> John
> >>
> >> On 24 February 2011 15:03, Simon Vandekar <[log in to unmask]> wrote:
> >> > Hi John and SPMers,
> >> >
> >> > I am attempting to normalise my fMRI data using the steps described in
> >> > pages 440 and 441 of the spm8 manual:
> >> >
> >> > 1. Slice timing
> >> > 2. Realign: Estimate and Reslice
> >> > 3. Coregister the structural to functional images
> >> > 4. Registration looks good.
> >> > 5. Segment the anatomicals the SPM5 routine
> >> > 6. Initial Import- use the *seg_sn files
> >> > 7. Run Dartel with dependency on the gray and white matter images
> output
> >> > by import step
> >> > 8. Normalise to MNI, select the template6 from dartel output, the
> >> > subject's flow field, and normalise the ra* files (slice timing,
> resliced).
> >> >
> >> > The output I get is sdra* files. When I compare the output to the mni
> >> > template it looks as if the subject's image has not been normalised. I
> am
> >> > suspicious of the flow field because if I look at the individual
> subjects'
> >> > uc1* image it is an empty black box.
> >> >
> >> > What am I doing incorrectly here?
> >> >
> >> > Thanks in advance,
> >> > Simon
> >> >
> >
> >
>