Hi Ken,
Thanks a lot for your reply. Here comes a follow-up question...
>> 1) About the input data, can I just directly feed the MRI scan to the
>> segmentation module? Sometimes, the input data may be very noisy, should I
>> first smooth the scan first before sending it to the segment module. Is
>> smoothing the scan a routine preprocessing step that a user should do
>> before doing segmentaiton?
>
> Just run it through and see if the result seems acceptable to you. If it
> looks
> like the segmentation worked well by eyeballing it, then you are good to go.
> If not, you have a few options.
>
> You CAN smooth it, but there are reasons it might not be the best idea. A
> Gaussian blur will smooth out the noise, but it will also smooth over the
> boundary between gray/white matter. Using another package that implements,
> say, a Kalman filter or other "adaptive" filtering scheme would be a
> preferable
> way to preprocess. But, probably the best way is to get more acceptable
> images.
I totally agree with what you said above. I asked this question because I
saw a "Smooth" button and curious if I should use it before segmentation.
> I don't know what your scanning parameters are, but there should be a way to
> get
> a high-quality whole brain anatomical image in not too much time. Have you
> asked your MR physicist to use an IR prepped T1 acquisition?
>
>> 2) About the output data, I noticed that the outputs on both the gray
>> matter and the white matter are not binary image. I wonder what does
>> different value for each voxel mean. In addition, how can I get a binary
>> mask of the gray matter and white matter?
>
> The values are the probability that each voxel is of a given tissue class.
> They
> should fall on the range [0 .. 1].
I just tried SPM5 on several datasets and the values are actually in the
range [0 .. 255] ( I selected the "Native space" option). Can I just
rescale them to let them fall on the range [0 .. 1]?
>> 3) Does SPM5 support extracting cerebral white matter and cerebral cortex
>> from the white matter and gray matter respectively?
>
> No, it doesn't do a cortical surface extraction like FreeSurfer does.
Thanks,
Kai
|