Thanks to Eugenio, for the tip!

We did look at (orig,nu,T1,brainmask,norm,nu,noneck, aseg, wm, filled).mgz. The only one showing a difference where our white matter error occurs is filled.mgz.
In some of the other previous images are minor differences around that area, but not overlapping the area. This starts with the brainmask.mgz. The wm.mgz looks almost identical though and this is what is used in making filled.mgz, right?

Cheers,
Mel and Vincent

P.S.: Here's a quick script to visualize all differences:
 
recon1='/data1/vbeliveau/atlas/proc/MR/recon/v0013_good'; %change this
recon2='/data1/vbeliveau/atlas/proc/MR/recon/v0013_bad'; %change this
dest='/data1/vbeliveau/atlas/test'; %change this

img1=MRIread([recon1 '/mri/orig/001.mgz']);
img2=MRIread([recon2 '/mri/orig/001.mgz']);
img1.vol=img1.vol-img2.vol;
MRIwrite(img1,[dest '/diff_raw.mgz']);
disp('raw');
sum(img1.vol(:)>10e-4)

vol={'orig','nu','T1','brainmask','norm','nu_noneck','aseg','brain','wm','filled'};

for n=1:numel(vol)
    img1=MRIread([recon1 '/mri/' vol{n} '.mgz']);
    img2=MRIread([recon2 '/mri/' vol{n} '.mgz']);
    img1.vol=img1.vol-img2.vol;
    MRIwrite(img1,[dest '/diff_' vol{n} '.mgz']);
    disp(vol{n});
    sum(img1.vol(:)>10e-4)
end
 



-------- Original Message --------
Subject: Re: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image
Date: Tue, 26 Aug 2014 14:05:19 +0200 (CEST)
From: Eugenio Iglesias <e.iglesias@bcbl.eu>
To: Melanie Ganz <Melanie.Ganz@nru.dk> 


It'd be really helpful if you looked at where the two pipelines start to diverge. It's apparent that the origs are the same, and that the surfaces are different, but where does the divergence begin? Are the nu.mgz's similar? How about the the brainmask.mgz's?
Here's the recon table: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

Best,
/E


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


----- Original Message -----
From: "Melanie Ganz" <Melanie.Ganz@nru.dk>
To: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, August 26, 2014 7:50:23 AM
Subject: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image

Dear Freesurfer community,

We've encountered a strange situation where the pial and wm surface 
delineation is successful for one image but contains wm (and subsequent 
pial) errors for another, almost identical structural image (see 
attached image, red and yellow are for the successful surface and blue 
and green are for the failed one). We've tried to identify the source 
for this discrepancy but I'm at a loss. All voxels of the original input 
images are identical to the 4th decimal and when converted to orig.mgz 
only a few voxels appear to be different due to rounding, none of which 
overlap with the wm surface errors. Both images were processed on the 
same setup (hardware and software, Freesurfer stable 5.3). 
Unfortunately, this error is quite systematic in my dataset; about 10% 
of the images show this type of error. Any suggestions on how to 
investigate this? I've uploaded example of good and bad at 
recon ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming/failed_wm_recon.tar.gz 
in case you'd like to have a closer look.

Thanks for your help.

Vincent and Melanie




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