Cate,
I can't seem to reproduce that bus error on our Intel Mac with plain data. Can you send me that subject in a tarball?
tar cvf mm103184.tar mm103184/ gzip mm103184.tar
You can upload it to me via our secure file drop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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