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 CautionHello.
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 rangeShould 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
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 > >
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