Question
Question Posted 07/24/13:
For ADNI1 FDG-PET scans, I have noticed that there are markedly fewer fully post-processed scans at months 18 and 24. That is, the last step in the post-processing pipeline (i.e., site-specific smoothing based on ADNI phantom) appears to have not been done for many participants. So I have, say, 270 fully post-processed baseline scans but only 65 fully post-processed month 24 scans. Even with mixed modeling, this may make publication difficult.
Thus, I have two questions:
1) Why was this homogenous smoothing post-processing step not followed for FDG images collected at months 18 and 24 in ADNI?
2) How have other groups gotten around this problem? Have they downloaded the FDG scans immediately prior to the final smoothing step, and then just used a single Gaussian to smooth them? That would seem like a terrible idea, because of the heterogenous smoothing of a raw FDG image based on the scanner used to collect it.
Thanks!
For ADNI1 FDG-PET scans, I have noticed that there are markedly fewer fully post-processed scans at months 18 and 24. That is, the last step in the post-processing pipeline (i.e., site-specific smoothing based on ADNI phantom) appears to have not been done for many participants. So I have, say, 270 fully post-processed baseline scans but only 65 fully post-processed month 24 scans. Even with mixed modeling, this may make publication difficult.
Thus, I have two questions:
1) Why was this homogenous smoothing post-processing step not followed for FDG images collected at months 18 and 24 in ADNI?
2) How have other groups gotten around this problem? Have they downloaded the FDG scans immediately prior to the final smoothing step, and then just used a single Gaussian to smooth them? That would seem like a terrible idea, because of the heterogenous smoothing of a raw FDG image based on the scanner used to collect it.
Thanks!
Response posted 07/24/13 by Susan Landau:
The smoothing of the FDG images that you are referring to (i.e. using a scanner-specific filter function) actually occurs during pre-processing and not post-processing.
PET pre-processing is described here (and also Joshi et al. Neuroimage 2009):
http://adni.loni.usc.edu/methods/pet-analysis/pre-processing/
So to download these FDG scans at uniform smoothness, you should identify the pre-processed FDG images with the image description "Coreg, Avg, Std Img and Vox Siz, Uniform Resolution."
PET pre-processing is described here (and also Joshi et al. Neuroimage 2009):
http://adni.loni.usc.edu/methods/pet-analysis/pre-processing/
So to download these FDG scans at uniform smoothness, you should identify the pre-processed FDG images with the image description "Coreg, Avg, Std Img and Vox Siz, Uniform Resolution."
Response posted 07/24/13 by Auriel Willette:
Thank you for the clarification.
As a follow-up question, I originally downloaded scans described as "Tx Origin, Aligned Baseline, Spatially Normalized, Smoothed". These scans are described as post-processed under 'type', referring to image type.
How do these scans differ from the Coreg, Avg, Std Img and Vox Siz, Uniform Resolution scans?
As a follow-up question, I originally downloaded scans described as "Tx Origin, Aligned Baseline, Spatially Normalized, Smoothed". These scans are described as post-processed under 'type', referring to image type.
How do these scans differ from the Coreg, Avg, Std Img and Vox Siz, Uniform Resolution scans?
Response posted 07/24/13 by Susan Landau:
Hello, The post-processed images you mentioned differ from the pre-processed images in that they are spatially normalized, meaning they have been warped into standard template space. Information about the spatial normalization of these post-processed images can be found in the Study Data section in the document called "Banner Alzheimer's Institute PET NMRC Summaries Methods (PDF)" or you can try contacting Kewei Chen at Banner.
