This isn't for an annotation automatically labelled using mris_ca_label; I've simply manually traced my ROIs then saved out an annotation by assigning labels from the colour table in tksurfer. At this stage I'd like to get stats on my manual ROIs. Does -b only give labels if the automatic parcellation is used? If so, would the order of ROIs appearing in the stats output table (e.g., the one below) always be the same as the order in the colour table?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
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From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sat 31/12/2005 12:54 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_anatomical_stats on custom annot
Hi Alex,
did you run mris_ca_train with -t <color table>? If so, it should embed the color table in the .gcs file, then get probagated to the .annot, so you shouldn't have to specify anything to mris_anatomical_stats.
cheers, Bruce On Fri, 30 Dec 2005, Fornito, Alexander wrote:
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
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