Dear Ben,
I would need to properly see your data to be able to help you with
this. Could you please upload the structural scan you are using as
well as the example_func file to
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and then send the six-digit number to my mail address (not the
mailbase).
Jesper
On 2 Jun 2010, at 20:19, Ben Yerys wrote:
> Hi FSLers--
>
> Thanks to Jesper and others for input on my registration woes.
> Removing the neck from the MPRAGE was one of several big problems in
> registering the High Res image to the Standard. However, I'm still
> having significant problems with registration. I do have a fair
> amount of ghosting in my images, because Fat Sat was turned off in
> order to have a sequence with TR=2000. At least I was told that Fat
> Sat had to be turned off for the sequence to be this fast.
>
> I've attached one picture which highlights my problem. It appears
> as though the EPI image is highly distorted in the right hemisphere
> (left side of display) and my thought is that this is driving all of
> my registration problems. I ran BET ("apply to 4D") with the
> default fractional intensity threshold of 0.5 to my 4D data and this
> removed almost all of the ghosting except for the two most superior
> slices and the distortion was reduced but still a problem. My other
> pre-processing steps include:
> MCFLIRT
> Slicetiming *I've taken this out in case I made a mistake in my
> slicetiming file
> Smooth FWHM
> Registration - Main structural image - Linear: Normal search with 6
> DOF
> Registration - Standard Space - Linear+Nonlinear with
> MNI152_T1_2mm_brain Warp Res=10mm
>
> The participant is a typically developing 12-yr-old who had a max
> translation movement of 0.5mm. I ran this data through SPM5 and
> from what I can see by eye using check reg, the registration looks
> acceptable and my activation map is in line with predictions for my
> set-shifting task. What am I missing?
>
> Thanks for the help!
> Ben
> <highres_to_standard_neck removed3.jpg>
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