On 12/18/2012 06:48 AM, Tudor Popescu wrote: > Dear all, > > I have some questions I could not find an answer to myself, I'd really > appreciate it if anyone could help out. > > 1) How should recon-all be used to process all subjects' data (i.e. > obtain the surface for each subject) before taking it to QDEC (or > command prompt) for a group thickness analysis? The QDEC tutorial > mentions a separate tutorial for the recon-all preprocessing part, but > it is not at all clear which one that is. Is there more to it than > just typing "recon-all --i file.nii –i file.dcm –subject bert –all" > for each subject (assuming NIFTI structurals)? To have it run through to the end, that is all you need (note that if file.nii and file.dcm represent the same volume, then only pass one). You will need to visually inspect and possibly manually fix your data. That is what the trouble shooting tutorial is about. > > 2) Is mri_glmfit FreeSurfer's equivalent of the randomise command in > FSL, i.e. it does nonparametric permutation-based inference based on > the given design matrix and produces statistical maps? Or are there > differences between the two in how the GLM is applied? mri_glmfit just performs the GLM analysis, ie, given an input y and a design matrix X and contrast matrices C1, C2, etc, it will fit the model to the data, compue beta's and residual variances, and test the contrasts, and computes parametric statistics. mri_glmfit-sim computes stats based on permutation or simulation stats. > > 3) Freeview and tksurfer seem to overlap in scope - when would you use > one rather than the other? Does it have to do with viewing structurals > vs statistically-generated maps? They do overlap a lot and there is on one case where you would use one over the other. freeview is newer, and tksurfer will eventually be phased out. > > 4) I see that points on reconall-generated surfaces are always > referred to in tutorials as vertices rather than voxels. Since both > represent the "unit of space", what exactly is the difference between > them? Conceptually, not much. "Vertex" is a term commonly used in mesh models in which the distance between the vertices is not fixed. "Voxels" comes from imaging. Really, they just represent different communities.
doug > > Many thanks in advance! > Tudor > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
