26 Mar
2019
26 Mar
'19
12:39 p.m.
overlay the orig.nofix on the data and see if it includes the non-brain tissue. You can also tar and gzip your entire subject dir and ftp it to us if you want us to take a look cheers Bruce
On Tue, 26 Mar 2019, Soichi Hayashi wrote:
External Email - Use Caution
Bruce, I am still going through the wiki, but I found the mri/brainmask.mgz contains a lot of non brain voxels like these..
Screenshot from 2019-03-26 11-56-48.png
Could this be the cause of the problem? Maybe Freesurfer had a problem generating a good brainmask? Does this create the high number of vertices that needs to be corrected?
Soichi
On Tue, Mar 26, 2019 at 10:46 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Soichi
look at the inflated.nofix in the 3D view, not the orig.nofix. You can check out our tutorial here:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev... gy%29%7C%28tutorial%29
although there may be a better one (hopefully someone else will chime in if so) cheers Bruce On Tue, 26 Mar 2019, Soichi Hayashi wrote: > > External Email - Use Caution > > Bruce, > Thank you for your help. I'd very much appreciate it. > > I've looked at rh.orig.nofix / rh.inflated.nofix, but I couldn't really find anything out of > ordinary.. from my layman's eyes. > > Screenshot from 2019-03-26 10-35-42.png > > Could you point me to the wiki you mentioned? > > Soichi > > On Sun, Mar 24, 2019 at 4:37 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Soichi > > that is too big a defect to expect it to fix - more than half the number > of vertices in a typical hemisphere. It means something is badly wrong > that you need to correct prior to the topo fixer. You can look at our > wiki for this kind of thing, but I would start by looking at the > rh.orig.nofix and the rh.inflated.nofix. Something big is wrong, like large > parts of the skull attached to the surface or something like that > > cheers > Bruce > > > On Sun, 24 Mar 2019, Soichi Hayashi wrote: > > > > > External Email - Use Caution > > > > Hello. > > I am trying to troubleshoot an issue where recon_all is not finishing after >24 hours. > It's getting > > stuck when it tries to run the following command. > > > > $ mris_fix_topology -rusage ./output/touch/rusage.mris_fix_topology.rh.dat -mgz > -sphere > > qsphere.nofix -ga -seed 1234 output rh > > INFO: assuming .mgz format > > reading spherical homeomorphism from 'qsphere.nofix' > > using genetic algorithm with optimized parameters > > setting seed for random number genererator to 1234 > > > > ************************************************************* > > Topology Correction Parameters > > retessellation mode: genetic search > > number of patches/generation : 10 > > number of generations : 10 > > surface mri loglikelihood coefficient : 1.0 > > volume mri loglikelihood coefficient : 10.0 > > normal dot loglikelihood coefficient : 1.0 > > quadratic curvature loglikelihood coefficient : 1.0 > > volume resolution : 2 > > eliminate vertices during search : 1 > > initial patch selection : 1 > > select all defect vertices : 0 > > ordering dependant retessellation: 0 > > use precomputed edge table : 0 > > smooth retessellated patch : 2 > > match retessellated patch : 1 > > verbose mode : 0 > > > > ************************************************************* > > $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ > > $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ > > reading input surface /home/hayashis/Downloads/output/surf/rh.qsphere.nofix... > > before topology correction, eno=-696 (nv=191488, nf=384368, ne=576552, g=349) > > reading brain volume from brain... > > reading wm segmentation from wm... > > using quasi-homeomorphic spherical map to tessellate cortical surface... > > > > Correction of the Topology > > Finding true center and radius of Spherical Surface...done > > Surface centered at (0,0,0) with radius 100.0 in 9 iterations > > marking ambiguous vertices... > > 133741 ambiguous faces found in tessellation > > segmenting defects... > > 63 defects found, arbitrating ambiguous regions... > > analyzing neighboring defects... > > -merging segment 16 into 0 > > -merging segment 23 into 0 > > -merging segment 48 into 0 > > -merging segment 32 into 22 > > -merging segment 49 into 47 > > -merging segment 54 into 51 > > 57 defects to be corrected > > 0 vertices coincident > > Computing Initial Surface Statistics > > -face loglikelihood: -9.3123 (-4.6561) > > -vertex loglikelihood: -6.5427 (-3.2713) > > -normal dot loglikelihood: -3.5794 (-3.5794) > > -quad curv loglikelihood: -6.0564 (-3.0282) > > Total Loglikelihood : -25.4907 > > > > CORRECTING DEFECT 0 (vertices=65141, convex hull=8287, v0=517) > > > > --------------- > > > > After displaying the last line, the process seems to be stuck running with 100% > cpu (single core) > > for >24 hours until our batch scheduler kills it. I think the issue is with my input > data, but it > > looks clean and well ACPC aligned, and I don't know what's wrong with it. The input > image dimensions > > are 182 x 218 x 182. > > > > Does anyone have any suggestion on how to troubleshoot this problem? > > > > Thank you, > > > > Soichi Hayashi > > Indiana University > > > > > > >