Re: [Freesurfer] mri_deface fails on pediatric brain

Hi Soichi

mri_deface isn't really supported anymore, but if you upload a subject that fails I'll take a look. I would have thought in the ABCD subject age range it would work

cheers Bruce On Sat, 3 Aug 2019, Soichi Hayashi wrote:

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Hello.

We are running mri_deface on subjects from ABCD (Adolescent Brain Cognitive Development) study and many of the subjects are failing on mri_deface.

  $ mri_deface t1.nii.gz
  $FREESURFER_HOME/average/talairach_mixed_with_skull.gca
  $FREESURFER_HOME/average/face.gca defaced.nii.gz
  logging results to defaced.nii.log
  reading
  '/usr/local/freesurfer/average/talairach_mixed_with_skull.gca'...
  reading 't1.nii.gz'...
  changing type of input volume to 8 bits/voxel...
  MRIchangeType: Building histogram
  bounding unknown intensity as < 10.3 or > 1461.6
  total sample mean = 111.8 (0 zeros)
  spacing=8, using 2055 sample points, tol=1.00e-03...
  resetting wm mean[0]: 143 --> 144
  resetting gm mean[0]: 89 --> 89
  input volume #1 is the most T1-like
  using real data threshold=11.0
  skull bounding box = (54, 38, 18) --> (205, 255, 220)
  using (104, 110, 119) as brain centroid...
  mean wm in atlas = 144, using box (85,83,94) --> (122, 136,143)
  to find MRI wm
  before smoothing, mri peak at 79
  robust fit to distribution - 80 +- 8.7
  distribution too broad for accurate scaling - disabling
  WARNING2: gca.c::GCAhistoScaleImageIntensities:
  h_mri->nbins=111, mri_peak=140
  after smoothing, mri peak at 0, scaling input intensities by
  inf
  GCAhistoScaleImageIntensities: could not find wm peak
  Numerical result out of range

Should talairach_mixed_with_skull.gca template work with pediatric subjects? Or is there a different template we must choose? Or maybe any parameters that we could tweak to get it work better?

Thanks! Soichi