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 
>
>