That area outside the brain is not present in both wm.mgz and filled.mgz for the failed output but for the good output, it is present in wm.mgz but not in filled.mgz (see attached figures). Again, given the similarity of the inputs it is surprising that the wm.mgz and filled.mgz end up being segmented so differently.
On 26.08.2014 23:41, Douglas N Greve wrote:
And is that area outside of the brain not present in
the wm.mgz or
filled.mgz on the good output? The orig.nofix should
hug the boundary of
the wm.mgz doug
On 08/26/2014 04:53 PM,
Vincent Beliveau wrote:
I've attached ?h.orig.nofix for both recon
with and without wm error. They are similar to ?h.orig in the sense that the one from the recon with wm error misclassifies part of dura as wm. Interestingly when looking at ?h.orig.nofix from the recon with error overlayed on brain.finalsurfs.mgz of the recon without error I can see a few voxels in the misclassified dura are removed from brain.finalsurfs, although not all. Could this small difference explain why we see the wm error in one case and not the other? On 26.08.2014 20:24, Douglas N Greve wrote:
how about the ?h.orig.nofix On 08/26/2014 10:45
AM, Vincent Beliveau wrote:
Dear Sebastian, Attached is the
*.orig for both recon (green being the one with wm error and red being the one with error). Unfortunately they are not identical; a section of the dura is misclassified as wm in the red delineation. As mentionned before, both orig.mgz are numerically identical in that area. As I also mentionned before, the recon were ran on the same machine, same os, same binaries. You expressed some confusion as to what were trying to achieve. We want to figure out why, given numerically almost identical inputs, Freesurfer correctly delineates wm in one case but fails in the other. Unfortunately this type of error appears to be systematic in some of our data. Vincent. On 26.08.2014 16:22, Sebastian Moeller wrote:
Hi Vincent hi Melanie, 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 [23]Melanie.Ganz@nru.dk>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;
I think the filled.mgz is changed during the generation of the wm surfaces (at least temporarily)...
in all the other
images the differences are minor.
Are you running the analyses on
exactly the same machine and get different results or are you using two "identical" computers? I ask as I think there is a paper about the reproducibility of freesurfer reconstructions (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038234 [24]) with different freesurfer versions or different hardware/operating systems that might explain a bit of systematic variance. But I guess I still do not exactly understand what the problem is that you want to solve here …. Best Regards Sebastian
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu [25] Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [26]
--
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu [27] greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 [28] www.nmr.mgh.harvard.edu/facility/filedrop/index.html [29] <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html [30]> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ [31] _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu [32] Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [33]
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu [34] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [35]
