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Dear Venkat, > Thanks very much does the same confirguration file work for T2 > weighted images too. Out T2 w images are 1*1*4. Any suggestions to > tweak some parameters. thanks again. it shouldn't matter if it is T1 or T2 (as long as you register like with like of course). What might matter a little is that your voxels are quite anisotropic. The configuration file I sent stops at a sub- sampling level of 2, i.e. had you had 1x1x1mm voxels it would have worked with 2x2x2mm averaged voxels at the highest level. That means that in your case it would use 2x2x8mm voxels at the highest level, and I am a little concerned that might lead to poor results in the z- direction. The simplest thing I would suggest would be for you to use applywarp to supersample your images up to 1x1x1mm resolution. As you do so make sure to use spline interpolation. After that you can use the configuration file I sent to perform the registration with fnirt, generating warp files. And then you apply those warp files to the original (non-supersampled) images. I hope that was clear. Jesper > > venkat > > ________________________________ > > From: FSL - FMRIB's Software Library on behalf of Jesper Andersson > Sent: Tue 5/4/2010 12:40 PM > To: [log in to unmask] > Subject: Re: [FSL] FNIRT- T2 weighted images between subjects > > > Dear Venkat, > > the following configuration file works well for registering high- > resolution T1 weighted images to one another. If you have a > reasonable high resolution (~1mm) and reasonably isotropic voxels I > think it should work well for you. Please let me know how it works. > > > =================================== > > P Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. >