Dear Greg,
On Tue, 9 Mar 2021 15:55:47 +0000, Kronberg, Greg <[log in to unmask]> wrote:
>Dear CAT12 users,
>
>Im using CAT12 version 12.7 with SPM12 version 7771 for a VBM analysis. After the segmentation step for most images, the cat12 automated report has poor ratings for the bias under "Image and Processing Quality." The ratings are typically around 65-70% with a grade of D+, which shows up in an ominous red color. I tried adjusting the "Power of SPM Inhomogeneity Correction" to strong and heavy, as well as affine preprocessing to full, but this didn't seem to help with the bias rating.
The estimated intensity inhomogeneity effects (bias) can be corrected very efficiently with CAT12 or SPM12 and this affects weighted average image quality rating (IQR) only o a minor extent. The bias rating will be unaffected by any settings in CAT12 because these parameters are obtained for the image before any preprocessing:
http://www.neuro.uni-jena.de/cat12-html/cat_methods_QA.html
Thus, I would keep the inhomogeneity corrections to the default value or probably change it to "strong", but would not change affine preprocessing parameters.
>
>The scans were collected a skyra 3T, 32 channel coil, at 0.8x0.8x0.8 mm resolution, without normalization filters.
Unfortunately, the default Siemens settings are not that appropriate. "Prescan Normalization" has a huge effect on your image inhomogeneity and it's damn efficient. However, it will be difficult to change that parameter for future acquisitions if you intend to mix the data. This might systematically affect your statistical analysis. If you don't mix old and new data enabling prescan normalization might be a good idea to largely improve image quality.
>
>I'm looking for some guidance on 1) how this rating is determined 2) any specific steps I can take to improve it 3) whether the results are usable as they are.
1) http://www.neuro.uni-jena.de/cat12-html/cat_methods_QA.html
2) see above
3) don't care too much if the IQR is fine
Best,
Christian
>
>I'm new to neuroimaging in general, so I may be missing something very basic.
>Any help would be greatly appreciated!
>
>Greg
>
>
>Greg Kronberg, PhD
>Postdoctoral Fellow
>Neuropsychoimaging of Addiction and Related Conditions (NARC) Lab
>Department of Psychiatry, Icahn School of Medicine at Mount Sinai
>
>
>
>
|