I think this is probably coming down to partial volume effects. Can you look at the underlying image to see whether cortex actually extends into the brown voxels?
On 4/15/19 3:54 PM, Caroline Chwiesko wrote: > > External Email - Use Caution > > Hello Douglas, > > that you very much for your quick response! I tried your suggestion > and it worked! > > However, when double checking my results I noticed something else, I > would like to ask about. > > The labels that I converted into volumetric space using mri_label2vol > with --fill-ribbon are nicely overlapping with the ribbon. > However, the labels, which I converted into volumetric space (and > which show the holes) using > mri_label2vol --annot BN_Atlas.annot --subject 1000 --hemi lh --o > xxxxxx/BN_Atlas.mgz --identity --temp xxxx/brain.mgz --proj frac 0 1 > 0.5 don t overlap exactly with the ribbon. > The latter contain voxels with values, that are 0 in the ribbon and 0 > in the labels converted in volumetric space with mri_label2vol. So, > the labels generated by mri_label2vol with --fill-ribbon and > mri_label2vol --annot BN_Atlas.annot differ and the difference is not > only the presence of holes in the latter. I attached two images for > illustration. > > My question is, why is this the case and which ones are the "better" > ones? The ones that overlap with the ribbon? > > Thank you very much in advance! > Carolin > > > Screen Shot 2019-04-12 at 5.29.44 PM.png > Screen Shot 2019-04-12 at 5.27.55 PM.png > > > > On Fri, Apr 12, 2019 at 7:48 AM Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > You can just multiply the output by the value of the index you > want, eg, > fscalc final.nii.gz -mul 5 -o final.5.nii.gz > Then give a different number to each label > > On 4/11/2019 9:08 PM, Caroline Chwiesko wrote: >> >> External Email - Use Caution >> >> Hello Freesurfers developers, >> >> I am very new to freesurfer. After getting the brainnetome >> parcellations using freesurfer, we need to convert the >> BN_Atlas.annot file from surface space into volumetric space. But >> the problem we have is that the converted labels have holes >> inside (see attached image 1). I am aware that this problem has >> been mentioned on this mailing list. But the suggested solution >> to use mri_label2vol –seg aparc + aseg.mgz will not work for us >> as the Brainnetome script does not output such files. We tried >> two different ways (see below), which did not result in success. >> >> 1.This command successfully brings the labels from surface to >> volumetric space but gives us the holes inside the labels. >> >> Mri_label2vol --annot BN_Atlas.annot --subject >> 1000 --hemi lh --o xxxx/xxx/xxxxx/xxxxx/BN_Atlas.mgz --identity >> --temp >> >> xxx/xxxxxx/xxxxx/brain.mgz --proj frac 0 1 0.5 >> >> >> 2.I emailed the Brainnetome authors and they suggested the >> command below. (In the command below I am trying to convert only >> 9 Brainnetome labels, just to see, if it will work). >> >> >> mri_annotation2label --subject 1001_20180507_MPRAGE --hemi lh >> --annotation BN_Atlas --sd >> /tmp/yassamri/R21/caro/Freesurfer/Freesurfer --labelbase >> >> /tmp/yassamri/R21/caro/Freesurfer/Freesurfer/1001_20180507_MPRAGE/test/lh.BN >> >> mri_label2vol --label lh.BN-000.label --label lh.BN-001.label >> --label lh.BN-003.label --label lh.BN-005.label --label >> lh.BN-007.label --label lh.BN-009.label --label lh.BN-009.label >> --label lh.BN-011.label --label lh.BN-013.label --subject >> 1001_20180507_MPRAGE --sd >> /tmp/yassamri/R21/caro/Freesurfer/Freesurfer/ --hemi lh >> --identity --fill-ribbon --o final.nii.gz >> >> >> This approach results in converted labels in volumetric space >> without holes, but all the labels have the value 1 (see attached >> image 2). But we need to keep the correct Brainnetome label >> values in volumetric space. What command/options could I use to >> overcome the problem with the holes and convert the file >> BN_Atlas.annot into volumetric space >> >> while keeping the Brainnetome label values? >> >> >> Thank you very much for your help in advance!! >> >> Carolin >> >> >> Our freesurfer version: >> >> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c >> >> we run it on Linux, kernel version 4.15.0-46-generic, Ubuntu >> 18.04.1 LTS >> >> >> image001.png >> Screen Shot 2019-04-11 at 5.46.19 PM.png >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
