Hi, I've been trying to export borders from subregions of the sensorimotor strip (suppl. Figure 8 of Glasser et al. 2016) to freesurfer annotation files (for visualisation in pySurfer).
Following the instructions in the FAQ (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?) I successfully translated the area labels (Figure 3, Glasser et al.) into corresponding freesurfer .annot-files (using mris-convert in the last step, as suggested here: https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446/2). My idea was to simply follow the same steps with the motor subregion borders by first transforming the borders to labels. I tried the following process: wb_command -border-to-rois $oldsphere $border $outdir/tmp.func.gii wb_command -border-export-color-table $border $outdir/label_list.txt wb_command -metric-label-import $outdir/tmp.func.gii $outdir/label_list.txt $outdir/tmp.label.gii -discard-others I then transformed the label file to freesurfer164 as I did with the other labels and converted the result to .annot with mris-convert. Unfortunately, the resulting annotation, after loading into tksurfer, shows nothing. Loading the annotation file with PySurfer returns the appropriate number of named labels, but these all contain the full set of vertices (with value=1). Roaming through the gifty-files a bit I noticed that the generated tmp.label.gii has each label as individual data column which is different from the set of full cortex labels which are defined as a single integer column. I guess that mris_convert does not process this structure properly. Is there a way to convert the multi-column label-gifty to the standard single-column label-gifty? Or is there a different way of exporting the borders to an appropriate freesurfer .annot-file? Thanks for your help! Sebastian Bitzer Chair of Neuroimaging TU Dresden http://sbitzer.eu/ _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
