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 Fischl fischl@nmr.mgh.harvard.eduwrote:
how do you know left/right is correct? In any case, if you upload the subject we'll take a look. Things very rarely fail that badly
On Mon, 1 Aug 2011, Christopher Luna wrote:
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 2012Desimone 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 youbring 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?
BruceOn 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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