I think what is happening is that when you use the --annot option, it will fill in a voxel even if the surface just barely goes through it. With --fill-ribbon, it will only fill in a voxel if that voxel is labeled as ribbon in the ribbon.mgz file. The --fill-ribbon is probably going to be more accurate (which seems to be the case in the images you sent). does that make sense?
On 4/16/19 4:54 PM, Caroline Chwiesko wrote: > > External Email - Use Caution > > Hi Douglas, > > Hi Douglas, > I attached 2 images. When I look just at the underlying anatomical > image, I would say it looks like the label voxel covers some white > matter as well. I marked those voxels with two arrows where it is most > easy to see/distinguish the white matter when I switch between > underlay and overlay. In the second image I have included additionally > the ribbon and it shows that those label voxels are not inside the ribbon. > > > > Screen Shot 2019-04-16 at 1.30.01 PM.png > > > > > Screen Shot 2019-04-16 at 1.28.47 PM.png > > On Tue, Apr 16, 2019 at 10:48 AM Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > 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> > <mailto: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> > <mailto: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> > <mailto: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 <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
