Hi Soichi

I have a fix for you. Can you let us know what kind of hardware/software env you are running in and we will send it to you?

cheers Bruce

On Sun, 4 Aug 2019, Soichi Hayashi wrote:

External Email - Use Caution

Bruce, I've uploaded one of the failed subject to surfer.nmr.mgh.harvard.edu ftp server (named t1.nii.gz).Thank you for looking into this problem.

Soichi

On Sun, Aug 4, 2019 at 10:35 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. -------

  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:

  >
  >         External Email - Use Caution        
  >
  > 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 
  >
  >