|
Size: 1238
Comment:
|
Size: 1527
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 11: | Line 11: |
| Possible contributing problems were (1) that the subject had a small brain to start with (2) that they were very obese, with alot of signal from fat around the scalp and neck (3) we did not reposition and reorient the images (eg with SPM display option) prior to normalisation. | The most likely problem in this specific case was (1) there was a lot of neck and shoulders, with some artifacts, near the bottom of the image (i.e, the field-of-view was probably too large) and (2) the image was a long way from the template (e.g, bad positioning of field-of-view). |
| Line 13: | Line 13: |
| Our solution (JBR and DE): For this participant, we used the SPM GUI 'normalize' procedure instead of the aamod_norm_noss (combined 'Segment and normalise') and write modules. Using Check registration (in SPM) the normalisation appeared OK | The best solution, though involving manual intervention, is to reposition the structural (via Display) so that it is closer to the template (ie origin = AC). Note that any functionals coregistered with the structural will also need to be repositioned the same way (using the "apply to" images in Display). If you want to stick with automated preprocessing, another solution is to use the SPM5 GUI 'normalize' procedure (i.e, normalisation as in SPM2) instead of the SPM5 'segment' procedure (ie not use aamod_norm_noss). |
Problem with two-pass normalisation
The standard aa normalisation routine ([http://imaging.mrc-cbu.cam.ac.uk/imaging/AutomaticAnalysisVersions#head-20f22d73e91b461dcf6bf69e792269bdce21ecf4 Automatic Analysis normalisation with segment]) may fail in certain cases. The example below illustrates it: at the bottom, the normalised brain on the left is smaller and has not been reoriented correctly.
If you look at the bottom right figure, supposedly of the GM segment, you will see that alot of her scalp has been segmented to GM by error (JBR).
attachment:norm_problem.jpg
In order to allow monitoring of such occurrences, please mail to imagerstech@mrc-cbu.cam.ac.uk if you notice this problem.
The most likely problem in this specific case was (1) there was a lot of neck and shoulders, with some artifacts, near the bottom of the image (i.e, the field-of-view was probably too large) and (2) the image was a long way from the template (e.g, bad positioning of field-of-view).
The best solution, though involving manual intervention, is to reposition the structural (via Display) so that it is closer to the template (ie origin = AC). Note that any functionals coregistered with the structural will also need to be repositioned the same way (using the "apply to" images in Display).
If you want to stick with automated preprocessing, another solution is to use the SPM5 GUI 'normalize' procedure (i.e, normalisation as in SPM2) instead of the SPM5 'segment' procedure (ie not use aamod_norm_noss).