Hi Satoshi,
Here's what we do with our (event-related) data in SPM2:
in SPM:
1) Reorient the data to the MNI space orientation (using "Display" and
"Reorient")
2) Slice timing correction
3) Realign --> Coregister and reslice --> Create mean image only
(creates meana*.img)
4) Coregister --> Coregister and reslice --> Target = meana*.img,
Source = structural image
in MRIcro:
"Open the images in MRIcro. The easiest way to do this is to
double-click on the mean image and your coregistered structural image in
the 'Windows explorer' - this should automatically open 2 windows of
MRIcro, one showing the mean image and the other the coregistered
structural. Yoke both images by ticking the box "Yoke" in the toolbar
section "Slice Viewer". In the window that shows the coregistered
structural, tick the box "Xbars" in the toolbar section "Slice Viewer".
If you now click at a brain area in the functional image you will see
the corresponding area in the structural (indicated by the
crosshairs)."
--> this is the quote from Matthew Brett's page, which is what we do,
although in the window with the structural image, rather than using the
x-bars, I like to load the functional image as an overlay to better see
the areas that need to be masked (go to Overlay --> Load image overlay
(meana*.img), and in the same menu, uncheck "opaque" so that you can see
the structural image underneath) - when doing this, you can clearly see
areas where there is brain meat, but no functional data (ie grey but no
red), and you mask these in the functional image. However, using the
crosshairs also works.
For the rest, I follow Matthew Brett's instructions.
Back in SPM2:
I go to Defaults --> Spatial Normalization --> Parameter Estimation -->
Weight template? NO --> Weight sources? YES
Then continue as normal, and during normalization, you will be asked
for your template, then your source image (meana*.img), then your source
weighting image, which is the mask you just created (mmeana*.img).
Hope this helps!
Dani
Daniel Simmonds
Developmental Cognitive Neurology
Kennedy Krieger Institute
[log in to unmask]
>>> Satoshi TANAKA <[log in to unmask]> 1/31/2007 3:50 PM >>>
Dear Experts,
On the following web page
http://imaging.mrc-cbu.cam.ac.uk/imaging/MaskedEpiNormalization,
we found an instruction how to do a Masking procedure for EPI
normalization. However, we noticed that the instruction is obviously
written for SPM99 because we cannot follow the instruction since SPM2
is
asking for something else (weighting template when registering?.
weighting source images when registering..etc.).
I would greatly appreciate your help.
Maybe you can give me the correct instructions for SPM2
in order to do the masking for the EPI normalization.
Thank you very much in advance.
Satoshi Tanaka
NINDS, NIH
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