no, the env variable won't change that. You can try changing the radius with:
-radius <n> where n=7 by default. Smaller will make it more aggressive. cheers Bruce On Mon, 5 Aug 2019, Brian Biekman wrote: > External Email - Use Caution > > I am also using pediatric brains and am also interesting in using your > defacing algorithm. I downloaded your updated script and changed the > environment variable but it leaves a lot of the jaw and chin. Is this > something that can be fixed by changing the environment variable to some > custom value? > > -- > Brian Biekman > Graduate Student, University of Houston > Clinical Psychology, Neuropsychology Concentration > Laboratory of Early Experience and Development (LEED) > bdbiek...@uh.edu > brian.biek...@times.uh.edu > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hoopes, Andrew > [ahoo...@mgh.harvard.edu] > Sent: Monday, August 05, 2019 12:25 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] [External] Re: mri_deface fails on pediatric brain > > Hi Soichi, you can update mri_deface with: > > curl > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos7_x86_64/mri_deface > -o $FREESURFER_HOME/bin/mri_deface > chmod +x $FREESURFER_HOME/bin/mri_deface > > Then, before running mri_deface, set the env variable: > > export FS_HISTO_STD_THRESH=20 > > Then, it should print out something like: > > mean wm in atlas = 144, using box (79,77,96) --> (120, 132,144) to find MRI > wm before smoothing, mri peak at 76 > FS_HISTO_STD_THRESH found in the environment resetting from 10 to 20.0 > robust fit to distribution - 76 +- 6.5 > after smoothing, mri peak at 76, scaling input intensities by 1.895 > mean wm in atlas = 144, using box (79,77,96) --> (120, 132,144) to find MRI > wm before smoothing, mri peak at 76 > FS_HISTO_STD_THRESH found in the environment resetting from 10 to 20.0 > robust fit to distribution - 76 +- 6.5 > after smoothing, mri peak at 76, scaling input intensities by 1.895 > > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Soichi Hayashi > <hayas...@iu.edu> > Sent: Monday, August 5, 2019 11:32 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] [External] Re: mri_deface fails on pediatric brain > > 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 > <fis...@nmr.mgh.harvard.edu<mailto:fis...@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 Caution >> >> Bruce, >> I've uploaded one of the failed subject to >> surfer.nmr.mgh.harvard.edu<http://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<mailto:fis...@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 >> > >> > >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
