Hi, I'm trying to run mris_anatomical_stats on a custom parcellation, but am having problems because I don't know what the flag to speficy the appropriate colour table is. If I run the -b option, I get output but with no labels. If I run -f, I get a message saying that no colour table is loaded. Commands and output are below. Thanks, Alex
mris_anatomical_stats -mgz -a acc.annot -b 1000908 lh white INFO: assuming MGZ format for volumes. computing statistics for each annotation in acc.annot. reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000908/mri/wm.mgz... reading input surface /data/flanders/work/alex/freesurfer/subjects_fe/1000908/surf/lh.white... INFO: Volume /tmp/mritotal_1614/nu_8_dxyz.mnc cannot be found. done. computing second fundamental form... ... done. total white matter volume = 442238 mm^3
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
111575 75355 185201 2.472 +- 0.836 0.190 0.061 1980.885 250.831 ** annotation 003c1400 444 269 715 2.685 +- 0.637 0.110 0.021 1.601 0.402 ** annotation 00dc3c3c 891 578 1588 2.777 +- 0.537 0.187 0.034 15.162 1.149 ** annotation 003c3c8c 213 126 392 3.145 +- 0.924 0.152 0.034 2.943 0.297 ** annotation 003c6464 82 40 152 3.785 +- 0.634 0.070 0.011 0.196 0.034 ** annotation 00b4648c 567 334 906 2.723 +- 0.503 0.103 0.020 2.385 0.434 ** annotation 00b48c3c 1093 709 2195 3.051 +- 0.793 0.206 0.078 20.688 3.225 ** annotation 003c643c 240 139 311 2.247 +- 0.872 0.085 0.010 0.454 0.149 ** annotation 008c143c
*OR*
mris_anatomical_stats -mgz -a acc.annot -f ./1000908.txt 1000908 lh white INFO: assuming MGZ format for volumes. computing statistics for each annotation in acc.annot. reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000908/mri/wm.mgz... reading input surface /data/flanders/work/alex/freesurfer/subjects_fe/1000908/surf/lh.white... INFO: Volume /tmp/mritotal_1614/nu_8_dxyz.mnc cannot be found. done. computing second fundamental form... ... done. total white matter volume = 442238 mm^3 mris_anatomical_stats: no color table loaded - cannot translate annot file
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au