Thanks for your response. I now have a question about applying the
normalization parameters from the normalized T1 (normalized with a
lesion mask) to the EPI time series data.
The T1 normalized with a very good outcome. I then went back and
coregistered (mutual information coregistration) the unnormalized T1 to
the mean realigned EPI and resliced the entire time-series.
The T1 and EPI are now in qualitatively anyway, near perfect register.
However, when I apply the normalization parameters to the EPI
time-series data and use Check Reg to inspect the spatially normalized
T1, a normalized EPI scan and the T1 template, the EPI scan its way out
of register with the others. It seems its origin is lower by several
slices.
Can you identify any misteps on my part? Should I be using the lesion
mask with the EPI time series data as well?
Thanks,
karl
John Ashburner wrote:
>>I have a question regarding the re-orientation of a lesion mask created
>>in MRIcro.
>>
>>1) I have created a lesion mask in MRIcro from a high-resolution T1.
>>(exported as smoothed Analyze image)
>>
>>2) I changed the orientation of the T1 from the display window in
>>SPM2. (slight pitch (.2 radians) and set origin to the AC)
>>
>>The lesion mask and T1 now have different orientations. Should I apply
>>the same origin and rotations to the lesion mask? I tried this and the
>>normalization routine failed, saying the images were not in the same
>>orientation.
>>
>>
>
>Make sure they are in alignment (using the Check Reg button). Once you are
>happy with this, then you can reslice the lesion mask to match the source
>image. You can do this with the reslice only via the Coregister button.
>
>Best regards,
>-John
>
>
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