This is the output for the parcellate_subject:
[autologins-Computer:stem/freesurfer/subjects] wanpark% parcellate_subject cf1 reading atlas from /Users/wanpark/Desktop/FreeSurfer/freesurfer/average/ lh.atlas2002_simple.gcs reading color table from GCSA file.... input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 15065 changed, 190865 examined... 001: 3883 changed, 57322 examined... 002: 1317 changed, 20293 examined... 003: 629 changed, 7437 examined... 004: 333 changed, 3451 examined... 005: 187 changed, 1811 examined... 006: 108 changed, 1054 examined... 007: 60 changed, 594 examined... 008: 37 changed, 330 examined... 009: 23 changed, 206 examined... 010: 23 changed, 130 examined... 011: 11 changed, 117 examined... 012: 10 changed, 67 examined... 013: 6 changed, 44 examined... 014: 1 changed, 27 examined... 015: 0 changed, 5 examined... 000: 678 total segments, 566 labels (9496 vertices) changed 001: 180 total segments, 70 labels (776 vertices) changed 002: 115 total segments, 5 labels (366 vertices) changed 003: 110 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 167 changed) writing output to /Users/../Volumes/stem/freesurfer/subjects/cf1/label/lh.aparc.annot... writing colortable into annotation file... classification took 20 minutes and 46 seconds. reading atlas from /Users/wanpark/Desktop/FreeSurfer/freesurfer/average/ rh.atlas2002_simple.gcs reading color table from GCSA file.... input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 14686 changed, 187213 examined... 001: 3723 changed, 54710 examined... 002: 1228 changed, 19135 examined... 003: 543 changed, 6751 examined... 004: 305 changed, 3107 examined... 005: 171 changed, 1740 examined... 006: 92 changed, 948 examined... 007: 48 changed, 498 examined... 008: 26 changed, 256 examined... 009: 18 changed, 153 examined... 010: 11 changed, 85 examined... 011: 8 changed, 49 examined... 012: 1 changed, 36 examined... 013: 0 changed, 8 examined... 000: 586 total segments, 459 labels (8211 vertices) changed 001: 166 total segments, 45 labels (461 vertices) changed 002: 122 total segments, 2 labels (19 vertices) changed 003: 120 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 196 changed) writing output to /Users/../Volumes/stem/freesurfer/subjects/cf1/label/rh.aparc.annot... writing colortable into annotation file... classification took 18 minutes and 52 seconds. [autologins-Computer:stem/freesurfer/subjects] wanpark%
and then the tksurfer cf1 rh inflated > file > label> import annotation
/Users/../Volumes/stem/freesurfer/subjects/cf1/label/rh.aparc.annot:
[autologins-Computer:stem/freesurfer/subjects] wanpark% tksurfer cf1 rh inflated surfer: current subjects dir: /Users/../Volumes/stem/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Volumes/stem/freesurfer/subjects surfer: /Users/../Volumes/stem/freesurfer/subjects/cf1/mri/T1/COR-.info ltMNIread: could not open file /Users/../Volumes/stem/freesurfer/subjects/cf1/mri/transforms/ talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=187213, faces=375476 surfer: using interface /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tksurfer.tcl Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tkm_common.tcl Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/fsgdfPlot.tcl Couldn't load libtclfsgdf.dylib. Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tkUtils.tcl Read /Users/wanpark/Desktop/FreeSurfer/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[1839]: arguments too large: 3221210976,520 CTABreadFrom: could not allocate -1073756320 bin table Cannot allocate memory Bus error
my machine is a mac dual 1 GHz PowerPC G4 2 MB L3 cache per processor, Memory 1.5 Gb SDRAM rh.annot.aparc is not a directory..
what i can do?
thanks
wan