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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