I’m trying to extract the surface area measurements for each subject from clusters generated by Monte Carlo analysis within qdec. From previous posts I came up with the following command:
mri_segstats --annot fsaverage lh mc-z.abs.th20.sig.ocn --i y.mgh --avgwf lh-Diff-HV-WAGR-Intercept-area.dat As an aside, the only way that this command would work was by copying the mc-z.abs.th20.sig.ocn.annot file within the contrast directory lh-Diff-HV-WAGR-Intercept-area to the fsaverage/label directory and renaming it to lh.mc-z.abs.th20.sig.ocn.annot. If I enter the absolute path of the annotation file into the command as follows: mri_segstats --annot fsaverage lh /Users/flalonde/Desktop/WAGR_freesurfer5.3/qdec/lh_10_area_WAGR_HV/lh-Diff-HV-WAGR-Intercept-area/mc-z.abs.th20.sig.ocn.annot --i y.mgh --avgwf lh-Diff-HV-WAGR-Intercept-area_full_path.dat I get the following error: Reading annotation could not read annot file /Users/flalonde/Desktop/WAGR_freesurfer5.3/fsaverage/label/lh./Users/flalonde/Desktop/WAGR_freesurfer5.3/qdec/lh_10_area_WAGR_HV/lh-Diff-HV-WAGR-Intercept-area/mc-z.abs.th20.sig.ocn.annot.annot No such file or directory ... trying local annot reading colortable from annotation file... colortable with 6 entries read (originally none) Successfully read local annot Oddly enough I get the same results in the avgwf file with either command. Pardon what might be a silly question but what are the values in the avgwf file? The columns seem to refer to individual clusters and the rows to individual subjects (presumably in the same order as the original qdec table used to generate the analysis) but the numbers range from 0 to 1. Thanks, François
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