[Freesurfer] error in the visualization of the parcellation
hi, i am using a mac G5. after successfully doing the talairach (thanks tosa and quinn) i went through and i did the parcellation: (last part) labeling surface... relabeling using gibbs priors... 000: 12553 changed, 169800 examined... 001: 3181 changed, 48112 examined... 002: 1021 changed, 16263 examined... 003:473 changed, 5771 examined... 004:281 changed, 2658 examined... 005:157 changed, 1570 examined... 006: 69 changed, 848 examined... 007: 34 changed, 397 examined... 008: 19 changed, 211 examined... 009: 9 changed, 120 examined... 010: 8 changed, 47 examined... 011: 8 changed, 49 examined... 012: 2 changed, 44 examined... 013: 0 changed, 11 examined... 000: 538 total segments, 417 labels (5917 vertices) changed 001: 158 total segments, 44 labels (399 vertices) changed 002: 116 total segments, 2 labels (13 vertices) changed 003: 114 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 172 changed) writing output to /usr/local/freesurfer_package/freesurfer/subjects/22970/label/rh.aparc.annot... writing colortable into annotation file... classification took 4 minutes and 49 seconds. i tried to see it and wrote: tksurfer 22970 rh inflated en then file> label> import annot> /usr/local/freesurfer_package/freesurfer/subjects/22970/label/rh.aparc.annot but i receive this message: [ogden:freesurfer_package/freesurfer/subjects] wpark% tksurfer 22970 rh inflated surfer: current subjects dir: /usr/local/freesurfer_package/freesurfer/subjects surfer: not in scripts dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer_package/freesurfer/subjects surfer: /usr/local/freesurfer_package/freesurfer/subjects/22970/mri/T1/COR-.info INFO: Src volume /tmp/mritotal_4912/orig_8_dxyz.mnc INFO: Target volume /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc INFO: Volume /tmp/mritotal_4912/orig_8_dxyz.mnc cannot be found. ncopen: filename /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc: Invalid dimension id or name miopen: MINC package entry point Error opening /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc mincRead(): error reading volume from file /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc surfer: vertices=169800, faces=339596 surfer: using interface /usr/local/freesurfer_package/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/fsgdfPlot.tcl Couldn't load libtclfsgdf.dylib. Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkUtils.tcl Read /usr/local/freesurfer_package/freesurfer/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[11526]: arguments too large: 3221210976,520 CTABreadFrom: could not allocate -1073756320 bin table Cannot allocate memory Bus error [ogden:freesurfer_package/freesurfer/subjects] wpark% could you please help me with this? thanks, wan___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error in the visualization of the parcellation
Can you send me the annotation file? On Thu, 3 Feb 2005, Wan Park wrote: hi, i am using a mac G5. after successfully doing the talairach (thanks tosa and quinn) i went through and i did the parcellation: (last part) labeling surface... relabeling using gibbs priors... 000: 12553 changed, 169800 examined... 001: 3181 changed, 48112 examined... 002: 1021 changed, 16263 examined... 003:473 changed, 5771 examined... 004:281 changed, 2658 examined... 005:157 changed, 1570 examined... 006: 69 changed, 848 examined... 007: 34 changed, 397 examined... 008: 19 changed, 211 examined... 009: 9 changed, 120 examined... 010: 8 changed, 47 examined... 011: 8 changed, 49 examined... 012: 2 changed, 44 examined... 013: 0 changed, 11 examined... 000: 538 total segments, 417 labels (5917 vertices) changed 001: 158 total segments, 44 labels (399 vertices) changed 002: 116 total segments, 2 labels (13 vertices) changed 003: 114 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 172 changed) writing output to /usr/local/freesurfer_package/freesurfer/subjects/22970/label/ rh.aparc.annot... writing colortable into annotation file... classification took 4 minutes and 49 seconds. i tried to see it and wrote: tksurfer 22970 rh inflated en then file label import annot /usr/local/freesurfer_package/freesurfer/subjects/22970/label/rh.aparc.annot but i receive this message: [ogden:freesurfer_package/freesurfer/subjects] wpark% tksurfer 22970 rh inflated surfer: current subjects dir: /usr/local/freesurfer_package/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer_package/freesurfer/subjects surfer: /usr/local/freesurfer_package/freesurfer/subjects/22970/mri/T1/COR- .info INFO: Src volume /tmp/mritotal_4912/orig_8_dxyz.mnc INFO: Target volume /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc INFO: Volume /tmp/mritotal_4912/orig_8_dxyz.mnc cannot be found. ncopen: filename /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc: Invalid dimension id or name miopen: MINC package entry point Error opening /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc mincRead(): error reading volume from file /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc surfer: vertices=169800, faces=339596 surfer: using interface /usr/local/freesurfer_package/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/fsgdfPlot.tcl Couldn't load libtclfsgdf.dylib. Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkUtils.tcl Read /usr/local/freesurfer_package/freesurfer/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[11526]: arguments too large: 3221210976,520 CTABreadFrom: could not allocate -1073756320 bin table Cannot allocate memory Bus error [ogden:freesurfer_package/freesurfer/subjects] wpark% could you please help me with this? thanks, wan -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
