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
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
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Douglas N Greve -
Peter Boulos