[Freesurfer] Large White Matter Areas Ignored In Surface Detection

ating surfaces after placing them, I found no significant difference in white matter detection. How do I ensure all of the white matter in my converted IMGs is identified? Thank you kindly, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Bruce, The orientations are correct - they weren't at first so I had to do a lot of work in tkregister2 to get the orientations correct. Unfortunately I only have access to the *.IMG and sometimes the *.HDR file for each subject. Christopher Luna MIT Brain and Cognitive Sciences, Cla

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Ah, I forgot about the left/right orientation. Where should I upload these files? Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Mon, Aug 1, 2011 at 12:23 PM, Bruce

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

I've uploaded the IMG and HDR files, they are named after my email address. Thank you kindly, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Mon, Aug 1, 2011 at 12:

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Bruce, Thank you very much! We'll get in contact with them. Best, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Mon, Aug 1, 2011 at 2:52 PM, Bruce Fischl wrote:

[Freesurfer] mri_segment optional flags problem

also takes the "0.6" to be in the input file name instead of brain.mgz. Is there another option I'm missing? Or have I unfortunately stumbled upon a small bug? Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Researc

Re: [Freesurfer] mri_segment optional flags problem

Thanks for your help! Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Fri, Aug 5, 2011 at 3:22 PM, Irwin, William wrote: > Bruce, > > Until it is determined if

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Okay, I've uploaded them as cdluna_whitematter_002.img and *.hdr. Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Tue, Aug 9, 2011 at 11:02 PM, Bruce Fischl

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Bruce, We tried to reverse A/P by reversing it the Talairach transform since recon-all wasn't able to do it automatically. I'm actually not sure how to reverse it in the IMG and HDR files. Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Ins

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

This fixed everything! Thank you! Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Wed, Aug 10, 2011 at 2:43 PM, Douglas N Greve wrote: > One thing you can try is to look