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:

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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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer