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:
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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 <fis...@nmr.mgh.harvard.edu>
wrote:
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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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