Re: [Freesurfer] Which T1 volume to use for coregistration with PET volume

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I see... what does the fix topology step expect from the wm.mgz meaning how is it testing it and what are the values it would accept... for example if we were to script an auto fill step which calls a program which works on wm.mgz between steps what would it have to do to make this work

With the second point about the location mattering in gliomas...I assume this has an impact on areas like the cingulate ....and hippocampus where the hemispheres and brainstem are separated ....if so can this be addressed....also are there other tricky areas....does the deep segmentation work if the brain is shifted ....and the basal ganglia are not near their atlas positions.....

Thanks in advance

Mike

On Tue, 1 Jan. 2019, 3:18 am Bruce Fischl <fischl@nmr.mgh.harvard.edu wrote:

I see. Getting FS working is going to be a case-by-case thing then. For holes extending into the ventricles you will probably need to fill the hole in the wm.mgz to make the topology closer to what we expect it to be. For the gliomas it depends on where they are cheers Bruce On Tue, 1 Jan 2019, Michael Sughrue wrote:

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In some cases this is a hole in the cortex extending to the

ventricle...in others it 8s a low grade

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glioma which substantially enlarges ....and distorts the cortex

On Tue, 1 Jan. 2019, 2:54 am Bruce Fischl <fischl@nmr.mgh.harvard.edu

wrote:

...

  Hi Matt

  yes, we have done this a number of times but of course it depends

a lot

...

  on the details of the abnormality so it is hard to give generic

advice

...

  cheers
  Bruce

  On Fri, 28 Dec 2018, Michael Sughrue
  wrote:

  >
  >         External Email - Use Caution
  >
  > Has anyone had success extracting surfaces of brains with

obviously abnormal

...

  > surfaces....post-surgical or very distorted cortices from tumor

etc....even if the

...

  extraction is
  > imperfect, is it possible to do with freesurfer and get

something imperfect but

...

  useable.
  > ....typically this gets hung up at the fix tesselation step.....
  > if this isnt possible presently, any suggestions about how to

create modify the source

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  code to
  > create such a tool?
  >
  > On Fri, Dec 28, 2018 at 8:49 PM Matthieu Vanhoutte <

matthieuvanhoutte@gmail.com>

...

  wrote:
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  >
  >       Dear Freesurfer’s experts,
  >
  >       I used mri_coreg command to coregister PET image onto T1

volume. Basically, this

...

  command
  >       coregister PET image onto orig.mgz volume (default

target). However, I wonder if

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  T1.mgz
  >       wouldn’t be a better target since it has been corrected

for inhomogeneities and

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  >       intensity normalized ?
  >
  >       Thanks for helping !
  >
  >       Best,
  >       Matt
  >
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