Wan, I will be emailing you a fixed version of the utility 'mris_ca_label', which you should put in the $FREESURFER_HOME/bin directory. It is called by parcellate_subject, and should properly save the annotation data.
Please be aware that the source of this bug was one that might cause trouble in other programs. I am currently going through the freesurfer source to look for similar problems. I'll post a link to the new Tiger build once I am confident that the bugs are squashed. Let me know if this mris_ca_label works for you. Nick On Mon, 2005-06-13 at 10:21 -0300, Wan Park wrote: > > > ______________________________________________________________________ > > Hello, I have been running freesurfer in G5 Macs with Panther. I was > able to parcellate and retrieve data of the different areas. > However, recently we changed the OS from Panther to Tiger. Since then, > I have the following problem: > > When I do mris_anatomical_stats: > > [ogden:freesurfer_package/freesurfer/subjects] wpark% > mris_anatomical_stats -b -a 14649/label/rh.aparc.annot 14649 rh > computing statistics for each annotation in > 14649/label/rh.aparc.annot. > reading > volume /usr/local/freesurfer_package/freesurfer/subjects/14649/mri/wm... > reading input > surface > /usr/local/freesurfer_package/freesurfer/subjects/14649/surf/rh.white... > INFO: Volume /tmp/mritotal_2576/orig_8_dxyz.mnc cannot be found. > INFO: found the orig volume (mri/orig) to get c_(ras) information for > src > INFO: added info to the surface. > done. > computing second fundamental form...reading colortable from annotation > file... > colortable with 0 entries read (originally ) > done. > total white matter volume = 509402 mm^3 > > table columns are: > number of vertices > total surface area (mm^2) > total gray matter volume (mm^3) > average cortical thickness +- standard error (mm) > integrated rectified mean curvature > integrated rectified Gaussian curvature > folding index > intrinsic curvature index > structure name > > 3758 2149 4165 1.950 +- 0.579 0.199 0.067 75.676 9.502 > ** annotation 003c148c > 2251 1174 3233 2.652 +- 0.702 0.200 0.081 67.771 6.118 > ** annotation 00b43cb4 > 1285 731 1674 2.284 +- 0.590 0.179 0.065 25.068 2.573 > ** annotation 003cdc14 > 1282 792 1629 2.076 +- 0.523 0.170 0.041 14.336 1.902 > ** annotation 00dc3c65 > 1304 794 1569 2.005 +- 0.501 0.190 0.044 19.070 2.299 > ** annotation 008c1415 > 306 137 291 2.137 +- 0.534 0.147 0.025 3.083 > 0.471 ** annotation 00b43c15 > 1604 935 1722 1.840 +- 0.477 0.203 0.070 34.702 3.964 > ** annotation 001414b4 > 2363 1479 3196 2.165 +- 0.602 0.160 0.035 27.198 3.101 > ** annotation 00b46465 > 2602 1659 3292 1.968 +- 0.729 0.189 0.052 47.088 5.998 > ** annotation 00b4b43f > 2299 1339 3348 2.510 +- 0.575 0.192 0.051 50.159 4.279 > ** annotation 00dcb4dc > 548 309 766 2.469 +- 0.454 0.165 0.043 5.623 > 0.997 ** annotation 00c8c80a > 1015 591 1455 2.481 +- 0.499 0.196 0.056 24.732 1.704 > ** annotation 0064dc8c > .......... > > Instead of having the name of different areas, I receive > "annotation..." > > Curiously, this does not happen if I do mris_anatomical_stats in > previously parcellated brains (before the new installation). This > happens when I parcellate_subject and then I try to get the info of > the areas. > > This is what I got when I parcellate: > > [ogden:freesurfer_package/freesurfer/subjects] wpark% > parcellate_subject 14649 > reading atlas > from > /usr/local/freesurfer_package/freesurfer/average/lh.atlas2002_simple.gcs... > reading color table from GCSA file.... > 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: 9935 changed, 137093 examined... > 001: 2397 changed, 37088 examined... > 002: 731 changed, 12222 examined... > 003: 340 changed, 4117 examined... > 004: 155 changed, 1818 examined... > 005: 88 changed, 871 examined... > 006: 47 changed, 459 examined... > 007: 28 changed, 255 examined... > 008: 19 changed, 160 examined... > 009: 12 changed, 97 examined... > 010: 10 changed, 64 examined... > 011: 5 changed, 64 examined... > 012: 3 changed, 27 examined... > 013: 2 changed, 19 examined... > 014: 1 changed, 9 examined... > 015: 0 changed, 6 examined... > 000: 340 total segments, 238 labels (3015 vertices) changed > 001: 123 total segments, 23 labels (316 vertices) changed > 002: 104 total segments, 4 labels (20 vertices) changed > 003: 100 total segments, 0 labels (0 vertices) changed > 10 filter iterations complete (10 requested, 164 changed) > writing output > to > /usr/local/freesurfer_package/freesurfer/subjects/14649/label/lh.aparc.annot... > writing colortable into annotation file... > classification took 3 minutes and 42 seconds. > reading atlas > from > /usr/local/freesurfer_package/freesurfer/average/rh.atlas2002_simple.gcs... > reading color table from GCSA file.... > 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: 9869 changed, 137521 examined... > 001: 2399 changed, 36932 examined... > 002: 698 changed, 12235 examined... > 003: 282 changed, 3952 examined... > 004: 150 changed, 1565 examined... > 005: 81 changed, 821 examined... > 006: 58 changed, 453 examined... > 007: 30 changed, 299 examined... > 008: 10 changed, 170 examined... > 009: 4 changed, 54 examined... > 010: 4 changed, 26 examined... > 011: 3 changed, 22 examined... > 012: 2 changed, 17 examined... > 013: 2 changed, 14 examined... > 014: 1 changed, 8 examined... > 015: 0 changed, 10 examined... > 000: 303 total segments, 200 labels (2164 vertices) changed > 001: 114 total segments, 14 labels (62 vertices) changed > 002: 100 total segments, 0 labels (0 vertices) changed > 10 filter iterations complete (10 requested, 127 changed) > writing output > to > /usr/local/freesurfer_package/freesurfer/subjects/14649/label/rh.aparc.annot... > writing colortable into annotation file... > classification took 3 minutes and 38 seconds. > [ogden:freesurfer_package/freesurfer/subjects] wpark% > > > Anybody please could help me? I am a little desperate... > > Wan Park > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
