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
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