please show us the *.orig surfaces on the critical slice. I predict that these will be identical, If so you can ignore everything except brain.finalsurfs.mgz. Are the two versions of this file identical around the area of mis-classified tissue? I predict that there will be a slight difference. Also if you take Vincent’s brain.finalsurf.mgz and put this into Melanie’s recon and redo the generation of the wm surfaces I predict that now Melinie’s version will show the same problem.

On Aug 26, 2014, at 16:08 , Melanie Ganz <Melanie.Ganz@nru.dk> wrote:

Hi Sebastian,

I'm afraid that the problem is slightly more complicated. The inputs to recon-all are almost numerically identical (to the 4th decimal); when converted to orig.mgz, all voxels which are not identical (about only 700 of all the 1677216 voxels) vary only by 1 due to rounding. Their distribution is sparse and do not overlap with the white matter errors. Can such a small source of variation give this kind of difference? Ok, Freesurfer uses some random initialization, however as far as I know the seed is not random and set to 1234. We have looked at all the outputs created before wm.mgz (orig,nu,T1,brainmask,norm,nu_noneck,aseg,brain,wm,filled) and the only one showing a differences overlapping the wm errors is filled.mgz;

in all the other images the differences are minor.

Thanks.

Vincent.


P.S.: I keep sending the mails, since Vincent has problems posting to the list. ;-)

On 26-08-2014 15:32, Sebastian Moeller wrote:

Hi Melanie,


I guess your post got me confused then, since you did not really explain what your figure shows. With the information from this post I assume that red and yellow are wm and pia respectively from and recon and blue and green are from the second.

On Aug 26, 2014, at 15:16 , Melanie Ganz <Melanie.Ganz@nru.dk> wrote:

Hi Sebastian,

it is clear to us how to fix this, this is not the issue here.

The issue is that my colleague and I ran the same image, he used the original dicom as source and I a nifti version prepared for other processing,

 Plain conversion of dicim to nifty or further processing?

and we get very different results! And this even thought the actual images vary quite a bit.

 Well some processes use random seeds, so if these differs between reckons and the intensity of the dura is close to threshold for skull stripping you got your problem right there. Have a look at the orig surfaces, if those do not show wrong wm-voxels in the dura its the refinement process later on that introduces this problem. You state in a later map that there are differences in brain mask.mgz, which I believe to be the input for the volume to use for image gradient based surface adjustments (actually brain mask.mgz should be a start of a chain that ends in brain.finalsurfs.mgz I believe). So from my understanding this makes all sense. But unfortunately is not going to help you...

So thanks for the input, but this does not explain our processing difference. Especially not, since the wm.mgz files are basically identical.

 Does not matter the wm.mgz gets turned into filled.mgz but these only define the orig surfaces lh.orig and rh.orig not the *.wm… I think that https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable gives a decent overview of the inputs and outputs of all freesurfer processing stages, (I guess you know that already).

Best Regards
 Sebastian

Cheers,
Melanie

On 26-08-2014 15:12, Sebastian Moeller wrote:

Hi Melanie,

this looks like your brain mask contains bright dura mater that gets mis-classified as white matter, this I assumed happened n the skull stripping step, If you edit the brain mask to exclude the offending dura you should be fine (or alternatively it might help to edit the wm.mgz so the voxels contain a value of 1 where the offending dura sits, but I am not sure that this will work) and then re-run the following steps of the recon. So have a look at brainmask.mgz. I assume with image you mean volume? I             believe this really is showing that  you might need to play with the skull-stripping process a bit to get rid of the sure better (or with your sequence so you get less signal from those structures in the first place ;) )

Best Regards
 Sebastian

On Aug 26, 2014, at 13:50 , Melanie Ganz <Melanie.Ganz@nru.dk> wrote:

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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Melanie Ganz, MSc, Ph.D.
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University of Copenhagen
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Melanie Ganz, MSc, Ph.D.

Neurobiology Research Unit

University of Copenhagen

Rigshospitalet

Rockefeller Center

Juliane Maries Vej 28/30, 3.

DK-2100 Copenhagen

Denmark

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e-mail: 

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