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, 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 12:16 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Christopher,

are you sure that the orientations are correct? That is, when you bring the orig.mgz up in tkmedit does the coronal view actually show the brain coronally? Img is a dangerous format to use as it doesn't contain orientation info. Do you have access to the data in some other format before it was convered to img?

Bruce



On Mon, 1 Aug 2011, Christopher Luna wrote:

Hello Freesurfers,
I'm putting *.IMG files into the program and after correcting talaraich transformations for them, I notice that when the reconstructions have completed, that there are
entire lobes of white matter absent from the surfaces detected and from the wm.mgz file. I went through my hand at first to manually fill in the missing white matter for
the first case, but after seeing how many were affected, I figured there was some setting I may be missing or some contrast level that may be off.

I had tried using control points, but after following the WIKI instructions on regenerating 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 2012Desimone Lab, McGovern Institute for Brain Research

MIT Archery Club
Alpha Kappa Psi Colony at MIT





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