Cate, It looks like the problem you are encountering with mris_anatomical_stats is one where the labels were created with a dev version of a utility, which uses a newer different colortable format. So you will need to use the 'dev' version of mris_anatomical_stats, found here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev Copy the file to your /Applications/freesurfer/bin directory, then type: cd /Applications/freesurfer/bin chmod a+x mris_anatomical_stats It seems to work on the data that you sent me. Nick On Fri, 2007-05-11 at 14:41 -0400, Catherine Hartley wrote: > Thanks, Nick! > > That seemed to be working fine until it tried to write the file, and > then I got the same bus error that I emailed about before. Is there > something I need to do with the color table when I create a new > parcellation. > > [catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats -f > mm103184/stats/lh.aparc.splitcingulate.stats -a mm103184/label/ > lh.aparc.splitcingulate.annot mm103184 lh inflated > computing statistics for each annotation in mm103184/label/ > lh.aparc.splitcingulate.annot. > reading volume /Applications/freesurfer/subjects/reruns/mm103184/mri/ > wm.mgz... > reading input surface /Applications/freesurfer/subjects/reruns/ > mm103184/surf/lh.inflated... > reading input surface /Applications/freesurfer/subjects/reruns/ > mm103184/surf/lh.pial... > reading input surface /Applications/freesurfer/subjects/reruns/ > mm103184/surf/lh.white... > done. > computing second fundamental form...reading colortable from > annotation file... > CTABreadFrom: could not allocate -2 bin table > Cannot allocate memory > Bus error > [catemac:freesurfer/subjects/reruns] cate% > > -Cate > > On May 11, 2007, at 2:32 PM, Nick Schmansky wrote: > > > Cate, > > > > As wacky as this may seem, you have to put the flagged options first, > > then the required items, otherwise the flagged options will be blindly > > ignored (it took me a while to figure this out in the code). So try: > > > > mris_anatomical_stats \ > > -f mm103184/stats/lh.aparc.splitcingulate.stats \ > > -a mm103184/label/lh.aparc.splitcingulate.annot \ > > mm103184 lh inflated > > > > Nick > > > > > > On Fri, 2007-05-11 at 13:39 -0400, Catherine Hartley wrote: > >> On May 11, 2007, at 1:38 PM, Catherine Hartley wrote: > >> > >>> Hi Jenni, > >>> > >>> This doesn't work either: > >>> > >>> [catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats > >>> mm103184 lh inflated -f mm103184/stats/ > >>> lh.aparc.splitcingulate.stats -a mm103184/label/ > >>> lh.aparc.splitcingulate.annot > >>> > >>> Any suggestions? > >>> > >>> Thanks, > >>> Cate > >>> > >>> On May 11, 2007, at 1:33 PM, Jenni Pacheco wrote: > >>> > >>>> Hi Cate, > >>>> > >>>> I think you have to use the -f flag to specify an output file, > >>>> otherwise it just prints to the screen. > >>>> > >>>> mris_anatomical_stats > >>>> usage: mris_anatomical_stats [options] <subject name> <hemi> > >>>> [<surface name>] > >>>> > >>>> This program measures a variety of anatomical properties > >>>> > >>>> valid options are: > >>>> > >>>> -i <low thresh> <hi thresh> - only consider thicknesses in > >>>> the specified range. > >>>> -l <label file> - limit calculations to specified > >>>> label > >>>> -t <thickness file> - use specified file for computing > >>>> thickness statistics > >>>> -a <annotation file> - compute properties for each label > >>>> in the annotation file separately > >>>> -b - tabular output > >>>> -f tablefile - table output to a file (different format than -b) > >>>> -log <log> - will write the stats into a file named <log> > >>>> -nsmooth <#> - will smooth the thicknessmap # of iterations > >>>> before using it > >>>> > >>>> > >>>> > >>>> Jenni > >>>> On Fri, 11 May 2007, Catherine Hartley wrote: > >>>> > >>>>> Hi, > >>>>> > >>>>> I'm trying to get the anatomical statistics for a new > >>>>> parcellation, ? h.aparc.splitcingulate.annot, I've created using > >>>>> mris_divide_parcellation. I've tried using mris_anatomical_stats > >>>>> with various argument structures (specifying output filenames, > >>>>> not specifiying output filenames) and can't seem to get it to > >>>>> write a ?h.aparc.splitcingulate.stats file. > >>>>> > >>>>> It generates and outputs summary statistics, but it does not > >>>>> write a .stats file to the stats directory: > >>>>> > >>>>> [catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats > >>>>> mm103184 lh inflated -a mm103184/label/ > >>>>> lh.aparc.splitcingulate.annot > >>>>> reading volume /Applications/freesurfer/subjects/reruns/mm103184/ > >>>>> mri/ wm.mgz... > >>>>> reading input surface /Applications/freesurfer/subjects/reruns/ > >>>>> mm103184/surf/lh.inflated... > >>>>> reading input surface /Applications/freesurfer/subjects/reruns/ > >>>>> mm103184/surf/lh.pial... > >>>>> reading input surface /Applications/freesurfer/subjects/reruns/ > >>>>> mm103184/surf/lh.white... > >>>>> done. > >>>>> computing second fundamental form... ... done. > >>>>> total white matter volume = 516178 mm^3 > >>>>> total surface area = 81462 mm^2 > >>>>> total gray matter volume = 230187 mm^3 > >>>>> average cortical thickness = 2.175 mm +- 0.836 mm > >>>>> average integrated rectified mean curvature = 0.025 > >>>>> average integrated rectified Gaussian curvature = 0.096 > >>>>> folding index = 9766.477 > >>>>> intrinsic curvature index = 937.896 > >>>>> [catemac:freesurfer/subjects/reruns] cate% > >>>>> > >>>>> Thanks for your help! > >>>>> > >>>>> -Cate > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer@nmr.mgh.harvard.edu > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>> > >>>>> > >>>>> > >>> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
