Yes, all we did in this case was change amygdala to hippocampus and in other cases white matter to hippocampus or vice versa.
Thomas Fink Doktorand & wiss. Mitarb. Lehrstuhl für Neuropsychologie Mail: thomas.f...@psy.lmu.de Phone: +49(0)89/2180-3123 On Tue, Jan 28, 2014 at 2:32 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > can you cc the list? So all you did was change some voxels from > hippocampus to amygdala? > > > On Tue, 28 Jan 2014, Thomas Fink wrote: > > Hi Bruce, >> >> Sorry, these were .tifs. Now they are... >> >> Thanks >> >> On Mon, Jan 27, 2014 at 11:48 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Thomas >> >> what format are these in? Can you include extensions in the >> files you send in the future? >> >> thanks >> Bruce >> On Mon, 27 Jan 2014, Thomas Fink wrote: >> >> Hi Bruce, >> >> At the moment we are interested in the volumes and >> thus we checked and >> corrected the aseg-file (corrections done as >> described in the >> RecommendedReconstructions). >> In the first attachment you can see the incorrect >> automatic segementation of >> the hippocampus and in the second what it looked >> like after our corrections, >> but before the new recon with the giant defect. >> >> Cheerio, >> Thomas >> >> On Thu, Jan 23, 2014 at 10:39 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Thomas >> >> when you say errors in the hippocampus do you >> mean the aseg or >> the surfaces? If the surfaces, don't worry >> about them as they >> are not used in the hippocampal region. You >> are probably >> connecting the temporal lobe to the main body >> of the white >> matter creating a giant defect. >> >> cheers >> Bruce >> On Mon, 20 Jan 2014, Thomas Fink wrote: >> >> >> Dear Freesurfer experts, >> >> We are using FS 5.1 and have several >> participants >> with errors in the >> segmentation of the hippocampus and >> other regions of >> the cortex. So far we >> did corrections to the hippocampus but >> in 10 out of >> 13 participants we got >> error messages listed below: >> >> Seven participants: >> >> ----- >> >> CORRECTING DEFECT 0 (vertices=74686, >> convex >> hull=1605) >> >> Excessive topologic defect encountered: >> could not >> allocate 390335770 edges >> for retessellation >> >> Cannot allocate memory >> >> Darwin NPSY.local 12.4.0 Darwin Kernel >> Version >> 12.4.0: Wed May 1 17:57:12 >> PDT 2013; >> root:xnu-2050.24.15~1/RELEASE_X86_64 >> x86_64 >> >> ----- >> >> One participant: >> >> ----- >> >> mhtVoxelList_Add(189, 240, 290, 260205): >> complete >> list too big! >> >> mhtVoxelList_Add(189, 240, 290, 260205): >> complete >> list too big! >> >> No such file or directory >> >> marking ambiguous vertices... >> >> Too many intersected faces for face >> 255461 (126442, >> 128896, 128873) >> >> No such file or directory >> >> Darwin NPSY.local 12.4.0 Darwin Kernel >> Version >> 12.4.0: Wed May 1 17:57:12 >> PDT 2013; >> root:xnu-2050.24.15~1/RELEASE_X86_64 >> x86_64 >> >> ----- >> >> One participant: >> >> ----- >> >> CORRECTING DEFECT 14 (vertices=33317, >> convex >> hull=1285) >> >> mris_fix_topology(26738) malloc: *** >> mmap(size=1212047360) failed (error >> code=12) >> >> *** error: can't allocate region >> >> *** set a breakpoint in >> malloc_error_break to debug >> >> Bus error >> >> Darwin NPSY.local 12.4.0 Darwin Kernel >> Version >> 12.4.0: Wed May 1 17:57:12 >> PDT 2013; >> root:xnu-2050.24.15~1/RELEASE_X86_64 >> x86_64 >> >> ----- >> >> One participant: >> >> ----- >> >> Correction of the Topology >> >> Finding true center and radius of >> Spherical >> Surface...done >> >> Surface centered at (0,0,0) with radius >> 100.0 in 11 >> iterations >> >> marking ambiguous vertices... >> >> 414500 ambiguous faces found in >> tessellation >> >> segmenting defects... >> >> Bus error >> >> Darwin NPSY.local 12.4.0 Darwin Kernel >> Version >> 12.4.0: Wed May 1 17:57:12 >> PDT 2013; >> root:xnu-2050.24.15~1/RELEASE_X86_64 >> x86_64 >> >> ----- >> >> The error log says in all cases that >> there is >> something wrong with the >> cerebellum. When we open the ?h >> inflated.nofix file >> then we see the >> cerebellum added (see attached file) in >> the >> hemisphere we made the edits. >> >> We have no clue if or what we are doing >> wrong and >> here are the steps we >> did: >> >> - open the files (tkmedit subject >> norm.mgz >> -aseg.mgz >> >> - Tool -> Configure Segmentation Brush >> info -> >> select the hippocampus -> add >> voxels >> >> - File -> save segmentation >> >> - run recon with "recon-all -autorecon2 >> -noaseg >> -autorecon3 -subjid subject >> -nuintensitycor-3T" >> >> So far we had no problems with our >> subjects for all >> the previous steps >> (recon after wm, pial, .... edits) and >> it did run >> smoothly. >> >> >> Any help would be greatly appreciated. >> >> Thomas Fink Mail: thomas.f...@psy.lmu.de >> >> >> >> >> The information in this e-mail is intended only for >> the person to whom >> it is >> addressed. If you believe this e-mail was sent to >> you in error and the >> e-mail >> contains patient information, please contact the >> Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the >> e-mail was sent to you >> in error >> but does not contain patient information, please >> contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> >> >> >>
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