Thanks Bruce, When you say the atlas itself is included in the Freesurfer distribution, do you mean there is a 3D version of it available in the download?
Also, I am not looking for the individual subjects' images, I just want a copy of the final atlas as a 3D image in analyze/nifti format. (i.e. in the same format as the Harvard-Oxford atlas that is downloaded with FSL). Thanks a lot. Daniel Ferreira 2012/10/3 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Hi Daniel, > > 1. Do you mean the atlas or the parcellation of your subjects? We cannot > distribute the individual subjects in the atlas as the data was collected > under an IRB long ago that didn't include this. The atlas itself (summary > statistics derived from those subjects) is included in the FreeSurfer > distribution. > > 2. The subcortical areas are the same, but not the cortical ones. That > cortical parcellation is quite coarse, and while we did implement it we > were never given permission to distribute the automated version, so it is > not part of FreeSurfer. The boundaries that we define are thus different > than that one (and since the Harvard-Oxford one is based on volumetric > labeling of folding patterns we found that it contained a bunch of errors > in which e.g. the wrong side of a sulcus was labeled) > > cheers > Bruce > > > > On Wed, 3 Oct 2012, Daniel Ferreira wrote: > > Dear experts, >> I have a couple of questions regarding the cortical parcellation atlas >> that >> is used in Freesurfer: >> >> 1) I would like to know if it is possible to obtain the Desikan-Killiany >> atlas in 3D analyze/nifti format. With each region of the brain assigned a >> discrete integer number (for example the all of the voxels of the left >> inferior temporal lobe have an intensity = 1, or the whole of the left >> hippocampus = 2). >> >> 2) Are the Harvard-Oxford cortical and subcortical atlases that can be >> downloaded with FSL the same as the cortical parcellation atlas that is >> used >> in Freesurfer? (i.e. are the neuroanatomical boundaries the same; does the >> left inferior temporal cortex in the Freesurfer cortical parcellation = >> the >> left inferior temporal cortex in the Harvard-Oxford atlas downloaded with >> FSL) >> >> Many thanks >> >> Daniel Ferreira >> >> >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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