Hi All,
I basically used the default values for my normalization
parameters, except that I didn't use any masks when registering because I
used the EPI template. Also, I normalized to 4X4X4 rather than 2X2X2.
When normalizing, I chose the mean aVoo1.img for each subject to
determine image parameters. I chose this image because when I realigned I
didn't create new realigned images. Rather, I updated the .mat files
that were generated for the aV images during slice timing.
Once again, the confusing thing is why the nornalization failed
for only 2 out of 8 subjects, given that I used the same parameters for
all 8 subjects. As I said earlier, one of the subjects appears to have
been tilted in the scanner so that their images were not collected
parallel to the AC-PC line. In fact, even the anatomicals look jagged at
the bottom edge, suggesting the slices were collected in a tilted
orientation. Is there a way to correct for this? I rotated the
anatomical images but that didn't remove the jagged diagonal edge at the
bottom. The second subject's anatomicals look pretty good to me. I'm
not sure why the normalization didn't work in this case.
If anyone has any suggestions, I'd appreciate it.
Thanks,
Daniel Weissman
> Hi Dan,
> It would be helpful if you emailed the list exactly what you did -
> did you change the defaults at all or did you just run using the defaults?
> Regards,
> Kent
> >
> > Hi All,
> > I recently normalized several brains and found that I had trouble
> > with 2 out of 8. In one case, the axial images were collected at a
> > slight angle away from the AC-PC line. In the other case, the
> > non-normalized images look fine (i.e., were collected parallel to the
> > AC-PC line). However, in both cases, the normalized images appear jagged
> > around the edges. Does anyone have any ideas about why this might be the
> > case? By the way, I used the EPI template to normalize.
> >
> > Thanks,
> > :> Daniel Weissman
> >
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Kent A. Kiehl, Ph.D.
> 2255 Wesbrook Mall
> Department of Psychiatry
> University of British Columbia
> Vancouver, B.C., Canada V6T 2A1
> office (604) 822-0777
> lab (604) 822-7070
> fax (604) 822-7756
> email [log in to unmask]
> http://www.psychiatry.ubc.ca/sz/nilab/personnel/kiehl
>
>
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