Cloud,

in this instance, the documentation is ahead of what is available in the public release. talairach_with_skull_2.lta will be available in the next release. in the current release (5.1, and prior), talairach_with_skull.lta is created in two places: during skullstrip, and during the skull-lta stage. in principle they were supposed to be identical, in practice they werent, and the lta created by the skull-lta stage it seemed would sometimes produce a better skullstrip than that created in the skullstrip stage, hence the necessity to separate them in naming. you can tell which is which by looking at the file creation time in the recon-all.log

Nick

On Fri, 2012-01-27 at 12:53 -0800, cloud.ctrl@me.com wrote:

In article http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix, it is mentioned that talairach_with_skull_2.lta is created during autorecon2, and that it can be useful when troubleshooting skull-strips, however I do not find talairach_with_skull_2.lta in the mri/transforms directory of any of my subjects. Has the processing been altered since the creation of this article or is my data incomplete? If incomplete, why? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer