FYI, Nick- It may be something to do with the 'comm' program on Mac OS X (assuming that you wrote the scripts on a UNIX machine), but the labels_intersect file doesn't quite work properly. However, I do get correct intersection results from the labels_union script by simply switching 'uniq -u' to 'uniq -d' and leaving everything else the same. Below you can see that there are identical lines in the two files, 'comm' doesn't find them, and 'uniq -d' does find them.
$ grep 42796 TEST.zero.label 42796 -22.144 -40.241 27.868 0.000000 142796 -4.945 52.116 -14.802 0.000000 $ grep 42796 aparc_labels/lh.postcentral.label 42796 -22.144 -40.241 27.868 0.00000 $ labels_intersect TEST.zero.label lh.postcentral.label Int.label $ head Int.label #!ascii label , from subject 17682 vox2ras=TkReg 0 $ labels_intersect_jim TEST.zero.label lh.postcentral.label JimInt.label $ head JimInt.label #!ascii label , from subject 17682 vox2ras=TkReg 1175 42796 -22.144 -40.241 27.868 0.000000 43946 -22.166 -39.570 28.120 0.000000 43953 -22.313 -39.961 27.481 0.000000 45154 -21.927 -37.868 29.306 0.000000 45167 -22.067 -38.462 27.645 0.000000 45168 -22.290 -38.809 28.096 0.000000 45173 -21.669 -38.528 26.871 0.000000 45174 -22.199 -39.236 27.196 0.000000 Also of note, if the 5th stats column in the label files are different, no union or intersection is correctly found. The labels generated by mri_surfcluster have the cluster pval from the monte carlo simulations in the 5th column, but the labels generated by mri_annotation2label just have zeros. It's easy enough to fix with sed, though. Thanks for the help! --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota Nick Schmansky wrote: > Jim, > > Attached are two scripts for getting the union or intersect of two label > files. > > Nick > > On Thu, 2009-08-27 at 20:32 -0500, James Porter wrote: >> Hello- >> >> Is there a simple way to obtain the intersection of two labels, output >> into a third label? Or the intersection of a label and an .mgh file >> output by mri_surfcluster? >> >> For instance, I have a cluster defined by mri_glmfit/mri_surfcluster >> that spans multiple anatomical regions, and I want to investigate the >> values from subsections of the cluster. That is to say, I want to run >> mris_anatomical_stats on only the section of my cluster that covers, >> say, precentral cortex but not caudal middle frontal or pars opercularis. >> >> I've tried several strategies without success. The most promising seemed >> to be just having mri_surfcluster output an aparc file, and then pass >> that aparc file into mris_anatomical_stats. However, that aparc just >> puts the very first region definition to every vertex. The same happens >> if I run mri_label2aparc on the labels output by mri_surfcluster. This >> happens no matter which LUT or ctab I use, i.e., with aparc.annot.ctab >> the whole volume gets labeled "bankssts" and with FreeSurferColorLUT.txt >> every vertex in the cluster volume gets labeled "Left-Cerebral-Exterior." >> >> I guess there are a few issues in this email, but the most important one >> to me is being able to run mris_anatomical_stats on the union of a >> cluster file and the individual regions from the standard aparc atlas. >> >> Any suggestions? >> >> Thanks in advance, >> --------- >> Jim Porter >> Graduate Student >> Clinical Science & Psychopathology Research >> University of Minnesota >> >> _______________________________________________ >> 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
