External Email - Use Caution Hi there, I have an animal brain's MRI with 3 volumes, each with a good resolution in one of the planes. (i. 768x768x88, ii. 768x768x150, iii. 768x768x140) As far as I understand freeSurfere doesn't have a 3D ihgh-res reconstruction tool, right? So I tried to reconstruct a high-resolution 3D volume with NiftyMIC ( [ https://secure-web.cisco.com/1pycZ_2SF5XqnaigDfeUBVSUx6el0NqrRFY73S86xcHKBmENAMDW0UImRthmw5ABzQXy4HbR5YvrmPrKqVtps7XvPuj-FM18syDXhXobeyvrjYZXzCWNWL5XrFc_x6F6sXZmNJiaiqVbTgleW5W_JFX66v_8fxOYC_3g0Abw3qcNVhxtjB-lKCNvkgLJTBNfRoIcFNdptMbIJnJJLw4ctFkad0nyy3QrWENp1yPh_-VKqjYY9w45GedHmEn_vICXVD7bRQL8wfM64bNFfHnw7J19BvbmjjLeCH7Qd0TqPUlRbcIblAFj6bGvn1TJXdj1sHiz8ZcMieEXj42iBoIrFCg/https%3A%2F%2Fgithub.com%2Fgift-surg%2FNiftyMIC | https://secure-web.cisco.com/1pycZ_2SF5XqnaigDfeUBVSUx6el0NqrRFY73S86xcHKBmENAMDW0UImRthmw5ABzQXy4HbR5YvrmPrKqVtps7XvPuj-FM18syDXhXobeyvrjYZXzCWNWL5XrFc_x6F6sXZmNJiaiqVbTgleW5W_JFX66v_8fxOYC_3g0Abw3qcNVhxtjB-lKCNvkgLJTBNfRoIcFNdptMbIJnJJLw4ctFkad0nyy3QrWENp1yPh_-VKqjYY9w45GedHmEn_vICXVD7bRQL8wfM64bNFfHnw7J19BvbmjjLeCH7Qd0TqPUlRbcIblAFj6bGvn1TJXdj1sHiz8ZcMieEXj42iBoIrFCg/https%3A%2F%2Fgithub.com%2Fgift-surg%2FNiftyMIC ] ), but unfortunately it didn't work for me.
My final goal is to get good tissue segmentation (pial-, grey-, and white-matter labels). So now I am considering rescaling one of the scans in a high-dim. space (768x768x768) using imresize3 (or something similar for interpolation) with MATLAB. The rescaling works, but the non-high-resolution planes turn out to be elongated. I am not sure how to get past this issue, and register the new rescale volume with one of the old ones (trying some params with mri_vol2vol might work?) At the end I want to visualize rescaled 3D volume on top of the original scans, so I can at least (semi-automatically and then) manually segment it. thanks in advance :) - malav Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391
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