Thank you Bruce and MIke! I was not really looking for something INSTEAD of manual inspection, but for a measure of the quality of my dataset similarly to what is reccomended for functional MRI (in that case a SNR below 100 can be considered a criterion of exclusion). What are the meaning of these metrics?
Thank you Angela
Hi Mike
I agree! It's really hard to detect e.g. the tip of the nose wrapping into occipital cortex. I was thinking more of the tools that generate pages of snapshots so you can quickly scan through datasets to find dramatic failures
cheers Bruce On Mon, 23 Nov 2015, Harms, Michael wrote:
In my experience, none of the quantitative "SNR/CNR" metrics available through various FS tools (some of which may be part of the QATools) replace the need to manually inspect the results. Some truly awful data may show up as "outliers", but you can't count on those values to flag all the data with problems.
cheers, -MH
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms@wustl.edu
On 11/23/15 11:16 AM, "angela.favaro@unipd.it" angela.favaro@unipd.it wrote:
Hi all,
I am starting to use QAtools in Freesurfer. The scripts are working well, but I have two problems:
- the interpretation of output is the first. Are there ranges of
normality for SNR and intensity? Could you please give me some reference or link about how to interpret these data? Or do I only need to look at outliers (or something similar)? My values are in the range between 19 and 25 (and the subject with 19 have problems at visual inspection). The script also outputs 'no outlier' in all my subjects. Which type of outliers is it referring to?
- I have also problems in getting snapshots, but I think this is due to
my poor experience with setting paths of ImageMagick. I am using a MAC OSX 10.6.8 and I used (tcsh) setenv MAGICK_HOME /Applications/ImageMagick-6.9.2/bin but probably this is not enough (any suggestion is greatly apreciated).
Thank you for any help you can give me
Best wishes
Angela
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