Hi Peter, what scanner are you using? You might be better off with using a 3T atlas. Spec -schwartzya3t-atlas with recon-all and see if that cleans it up. You can run just the talairaching with
recon-all -s subject -schwartzya3t-atlas -talairach doug On 06/11/2013 01:03 PM, Peter Boulos wrote: > I am very new to the software and have just begun assessing Talairach > outputs for my subjects. I am confused in that I cannot seem to find a > balance I am happy with between positioning of the green lines in both > the horizontal and sagittal views for multiple subjects. I opened the > talairach output with the following command (tkregister2 --mgz --s > SUBJID --fstal --surf orig) and everything looked perfectly aligned > for all the subjects I have tried in both the coronal and sagittal > views but in the horizontal view the green lines went well off the > back of the brain. I have attached a screenshot. I tried to translate > the brain but that did not seem to solve my issue and I realized I > needed to scale the length of the brain. When I did that I was more > pleased with the outcome but the corpus callosum did not match up > nearly as well after I did that (second attached screenshot) and that > was the primary landmark I was using to pass my images in terms of > talairach output assessment. Do you have any advice for me? > > Peter > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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.
