Thank you, that explained a lot! I have used your procedure to get labels from the ROIs and it works beautifully. Following up on your warning about possible problems in extraction of ROIs from borders I have checked the generated labels against the original borders on the fs32 sphere and found very good correspondence between the two, certainly for my intended purpose.
Sebastian On 27/10/17 22:34, Timothy Coalson wrote: > The -*-label-import commands do not convert from separate ROIs to > single-map label format, because ROIs could overlap while labels are > not allowed to. You need to first create a file with a single map of > different integers for each ROI, before using these commands. > > First, you need to ensure that you actually have reasonable ROIs, as > even with what you did, you should still get one ROI per label map if > the inputs were what they should have been. Open the tmp.func.gii > file and make sure they actually have reasonable ROIs. The > -border-to-rois command is intended only for use on closed borders > (draw the entire boundary of the desired ROI), so if the borders were > simply lines across the motor strip, it will likely not behave well. > > If you don't care about how any overlapping vertices from the ROIs > get resolved, you can make ROIs into the needed one-integer-per-area > format like this: > > wb_command -metric-reduce rois.func.gii INDEXMAX indexmax.func.gii > wb_command -metric-reduce rois.func.gii MAX max.func.gii wb_command > -metric-mask indexmax.func.gii max.func.gii integers.func.gii > > Then -metric-label-import will do what is expected. Note, however, > that freesurfer annot files have the additional restriction that all > colors must be unique, as they use the color as the label key. > > Tim > > > On Fri, Oct 27, 2017 at 8:50 AM, Sebastian Bitzer > <sebastian.bit...@tu-dresden.de > <mailto:sebastian.bit...@tu-dresden.de>> wrote: > > 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 > <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 > <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 HCP-Users@humanconnectome.org > <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
