External Email - Use Caution
We run on our freesurfer through singularity/docker container, and we are currently using Centos7 as the base image to build our freesurfer container, but we can run it on any other Linux based OSes. As far as our hardware goes, we run on variety of hardware including HPC system, public and private cloud platforms and a few dedicated desktop machines at our labs.
Thanks! Soichi
On Sun, Aug 4, 2019 at 10:55 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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 CautionBruce, 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 > >