Re: [Freesurfer] source of thickness information for mris_preproc
Lars, The mris_preproc script uses the ?h.thickness files under the surf directories. N. On Fri, 2006-07-21 at 06:55 +0200, Lars M. Rimol wrote: > Hi, > When one runs mris_preproc with e.g. -meas thickness, does it get the > thickness information from the files in the stats directory within > each subject's directory - or from the ?h.thickness files under the > surf directories? > > > Thank you! > -- > yours, > LMR > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FLASH atlas
Hello, I read in the archive that you were planning on releasing two new atlases (for MP-RAGE and FLASH) last year. Were those (or even newer ones) distributed? I have some FLASH sequences I want to run. Thanks! -Derin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] source of thickness information for mris_preproc
>From mris_preproc --help : --meas surfmeasure Use subject/surf/hemi.surfmeasure as input. For use with --s, --fsgd, or --f. Implies --srcfmt curv. Lars M. Rimol wrote: Hi, When one runs mris_preproc with e.g. -meas thickness, does it get the thickness information from the files in the stats directory within each subject's directory - or from the ?h.thickness files under the surf directories? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FLASH atlas
Hi Derin, we actually made enough progress on the cross-sequence segmentation problem that we decided to just go with the mp-rage atlas. It works quite well these days. cheers, Bruce On Fri, 21 Jul 2006, Derin Cobia wrote: Hello, I read in the archive that you were planning on releasing two new atlases (for MP-RAGE and FLASH) last year. Were those (or even newer ones) distributed? I have some FLASH sequences I want to run. Thanks! -Derin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] label coordinates
Kevin has changed the way freesurfer writes labels. Previously, the coordinates were from the orig surface. From now on (in the development distribution) they will correspond to the white surface. As Kevin points out, the surface from which the coordinates were derived will be in the first line of the label file to help us keep track of the change. doug Original Message Subject: [Fsdev] tksurfer labels now written in white space Date: Fri, 21 Jul 2006 10:48:10 -0400 From: Kevin Teich <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] I changed label.c and label.h to add a text field. The LabelToXXX functions write a note to that field, "coords=XXX". LabelWrite now writes this field in the comment line of the label. I replaced all calls to LabelToOriginal in tksurfer with calls to LabelToWhite. -- Kevin Teich ___ Fsdev mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fsdev -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all malloc error
recon-all exited with the following error. Running on a Powermac G5 with 1G ram. Any ideas? thanks, Rutvik - Fix Topology rh Thu Jul 20 13:29:52 CDT 2006 /usr/local/freesurfer/subjects/2628/scripts mris_fix_topology 2628 rh reading input surface /usr/local/freesurfer/subjects/2628/surf/rh.qsphere... before topology correction, eno=-510 (nv=191807, nf=384696, ne=577013, g=256) using quasi-homeomorphic spherical map to tessellate cortical surface... mris_fix_topology(124) malloc: *** vm_allocate(size=2075615232) failed (error code=3) mris_fix_topology(124) malloc: *** error: can't allocate region mris_fix_topology(124) malloc: *** set a breakpoint in szone_error to debug could not allocate 16108 edges for retessellation Cannot allocate memory reading T1 volume from T1... reading wm segmentation from wm... 136542 ambiguous faces found in tessellation 246 of 4410 overlapping edges discarded 1 of 299 overlapping edges discarded 175 of 1655 overlapping edges discarded retessellating defect 3 with 4269 vertices (convex hull=26247). 661414 of 8448632 overlapping edges discarded 7 of 59 overlapping edges discarded 0 of 45 overlapping edges discarded retessellating defect 6 with 16108 vertices (convex hull=7747). ERROR: mris_fix_topology exited with non-zero status ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all malloc error
Hi Rutvik, we normally recommend 2G. The problem here though is something big - probably either the skull or the cerebellum attached to your surfaces. You'll need to find and detach it (the "136542 ambiguous faces found in tessellation" is way too many, and the # of vertices and faces (191807, 384696) is also way too many. Should be more like 120K vertices. cheers, Bruce On Fri, 21 Jul 2006, Rutvik Desai wrote: recon-all exited with the following error. Running on a Powermac G5 with 1G ram. Any ideas? thanks, Rutvik - Fix Topology rh Thu Jul 20 13:29:52 CDT 2006 /usr/local/freesurfer/subjects/2628/scripts mris_fix_topology 2628 rh reading input surface /usr/local/freesurfer/subjects/2628/surf/rh.qsphere... before topology correction, eno=-510 (nv=191807, nf=384696, ne=577013, g=256) using quasi-homeomorphic spherical map to tessellate cortical surface... mris_fix_topology(124) malloc: *** vm_allocate(size=2075615232) failed (error code=3) mris_fix_topology(124) malloc: *** error: can't allocate region mris_fix_topology(124) malloc: *** set a breakpoint in szone_error to debug could not allocate 16108 edges for retessellation Cannot allocate memory reading T1 volume from T1... reading wm segmentation from wm... 136542 ambiguous faces found in tessellation 246 of 4410 overlapping edges discarded 1 of 299 overlapping edges discarded 175 of 1655 overlapping edges discarded retessellating defect 3 with 4269 vertices (convex hull=26247). 661414 of 8448632 overlapping edges discarded 7 of 59 overlapping edges discarded 0 of 45 overlapping edges discarded retessellating defect 6 with 16108 vertices (convex hull=7747). ERROR: mris_fix_topology exited with non-zero status ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all malloc error
Hi Rutvik, Have you looked at your surfaces, is there a problem with the rh that you may need to fix manually before trying the topology fixer again? Jenni On Fri, 21 Jul 2006, Rutvik Desai wrote: recon-all exited with the following error. Running on a Powermac G5 with 1G ram. Any ideas? thanks, Rutvik - Fix Topology rh Thu Jul 20 13:29:52 CDT 2006 /usr/local/freesurfer/subjects/2628/scripts mris_fix_topology 2628 rh reading input surface /usr/local/freesurfer/subjects/2628/surf/rh.qsphere... before topology correction, eno=-510 (nv=191807, nf=384696, ne=577013, g=256) using quasi-homeomorphic spherical map to tessellate cortical surface... mris_fix_topology(124) malloc: *** vm_allocate(size=2075615232) failed (error code=3) mris_fix_topology(124) malloc: *** error: can't allocate region mris_fix_topology(124) malloc: *** set a breakpoint in szone_error to debug could not allocate 16108 edges for retessellation Cannot allocate memory reading T1 volume from T1... reading wm segmentation from wm... 136542 ambiguous faces found in tessellation 246 of 4410 overlapping edges discarded 1 of 299 overlapping edges discarded 175 of 1655 overlapping edges discarded retessellating defect 3 with 4269 vertices (convex hull=26247). 661414 of 8448632 overlapping edges discarded 7 of 59 overlapping edges discarded 0 of 45 overlapping edges discarded retessellating defect 6 with 16108 vertices (convex hull=7747). ERROR: mris_fix_topology exited with non-zero status ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all malloc error
Rutvik, Can you send the entire recon-all.log? thanks, Nick On Fri, 2006-07-21 at 15:15 -0400, Rutvik Desai wrote: > recon-all exited with the following error. Running on > a Powermac G5 with 1G ram. Any ideas? > > thanks, > Rutvik > > - > Fix Topology rh Thu Jul 20 13:29:52 CDT 2006 > /usr/local/freesurfer/subjects/2628/scripts > mris_fix_topology 2628 rh > reading input surface > /usr/local/freesurfer/subjects/2628/surf/rh.qsphere... > before topology correction, eno=-510 (nv=191807, nf=384696, ne=577013, > g=256) > using quasi-homeomorphic spherical map to tessellate cortical surface... > mris_fix_topology(124) malloc: *** vm_allocate(size=2075615232) failed > (error code=3) > mris_fix_topology(124) malloc: *** error: can't allocate region > mris_fix_topology(124) malloc: *** set a breakpoint in szone_error to > debug > could not allocate 16108 edges for retessellation > Cannot allocate memory > reading T1 volume from T1... > reading wm segmentation from wm... > 136542 ambiguous faces found in tessellation > 246 of 4410 overlapping edges discarded > 1 of 299 overlapping edges discarded > 175 of 1655 overlapping edges discarded > retessellating defect 3 with 4269 vertices (convex hull=26247). > 661414 of 8448632 overlapping edges discarded > 7 of 59 overlapping edges discarded > 0 of 45 overlapping edges discarded > retessellating defect 6 with 16108 vertices (convex hull=7747). > ERROR: mris_fix_topology exited with non-zero status > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
