On 24 February 2011 16:27, simon vandekar <[log in to unmask]
> 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,
> On Thu, Feb 24, 2011 at 10:47 AM, John Ashburner <[log in to unmask]
>> 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,
>> On 24 February 2011 15:03, Simon Vandekar <[log in to unmask]
>> > 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