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Could you post the GM probability maps along with their T1 images? It's hard to tell exactly where the problem is without that. ________________________________________ From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Lúcia Garrido [[log in to unmask]] Sent: Wednesday, July 18, 2012 7:56 PM To: [log in to unmask] Subject: [SPM] new segmentation and dartel Hello, I've been using new segmentation and had a few questions that I'd be very grateful if someone could answer or had any suggestions. I've done new segmentation and I think for many subjects it didn't work very well well. I've attached one example and there are many other subjects like this. It seems like the regions of the inferior temporal lobes were not segmented very well. I used the default options in new segment, so I used: - bias regularisation: 'very light regularisation (0.0001) - bias FWHM: 60mm cutoff - Used the tissue probability maps in TPM, 1 to 6, with these respective number of Gaussians: 2, 2, 2, 3, 4, 2. - MRF parameter: 0 - Warping regularisation: 4 - Sampling distance: 3 So my questions are: 1. Do you have any suggestions about what I can do differently to get better segmentation? 2. Has anyone varied the parameters above systematically and would be willing to share what they found with the list? I know that any results are going to depend a lot on the data we have, but I'd appreciate any insights about the different parameters. The manual is very helpful in explaining the different parameters, but I'd like to get a better idea about the effects of each of them. Moreover, for certain parameters, I'm not sure even how to vary them. In particular, for the MRF parameter, warping regularisation, and sampling distance, I'm not sure within which intervals these parameters can vary... 3. I also have a question about dartel, and I'm sorry if this sounds trivial... In the manual, it says that dartel takes about one week for 400 subjects. But I've run dartel with around 200 subjects and it took about 8 hours. I have an iMac with 2.8 GHz i7, and 16GB ram. It seems it should take longer than 8 hours, and was wondering if that estimation of a week was from a long time ago... I'm also happy that dartel takes more time if the registration results are better. So if someone has any advice about this, I'd really appreciate your help. The parameters I've been using for dartel are the default ones: - regularisation form: linear elastic energy - 6 outer iterations, each with 3 Gauss-Newton iterations, default regularisation parameters, time steps (varying from 1 to 64), and smoothing parameters - default optimisation settings Like for the segmentation case, I'd very much appreciate any information about the results of varying any of these parameters. Many thanks and best regards. Lucia Lúcia Garrido Post-Doctoral researcher Vision Sciences Laboratory Harvard University [log in to unmask]<mailto:[log in to unmask]> http://sites.google.com/site/garridolucia/