28 Jan
2014
28 Jan
'14
8:40 a.m.
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.Fink@psy.lmu.de Phone: +49(0)89/2180-3123
On Tue, Jan 28, 2014 at 2:32 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
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 < fischl@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 <fischl@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.Fink@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.
28 Jan
28 Jan
8:49 a.m.
New subject: Fwd: Corrections to the segmentation lead to giant defects
changing amygdala to hippocampus shouldn't change the surfaces at all. If you upload the subject I'll take a look
On Tue, 28 Jan 2014, Thomas Fink wrote:
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.Fink@psy.lmu.de Phone: +49(0)89/2180-3123
On Tue, Jan 28, 2014 at 2:32 PM, Bruce Fischl fischl@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 <fischl@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 <fischl@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.Fink@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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Bruce Fischl -
Thomas Fink