External Email - Use Caution Now, I understand! Thank you so much for your help !! ;-)
Carolin On Tue, Apr 16, 2019 at 4:07 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > A voxel is a 3D cube. The surface is a 2D sheet. The surface may pass > through the cube in several ways. It might pass right through middle or > just nick one of the corners. When we select whether the voxel is > inside or outside of the surface, we have to handle these cases where it > is partially in the voxel. --fill-ribbon will require that most of the > voxel be within the surface. --annot will determine that the voxel will > be inside the surface even if the surface just nicks it. > > On 4/16/19 6:58 PM, Caroline Chwiesko wrote: > > > > External Email - Use Caution > > > > Could you explain a little more what you mean with "even if the > > surface just barely goes through it"? > > I assume that this is something I would understand when I look in more > > detail on how the conversion is done from surface to volumetric space? > > > > Carolin > > > > On Tue, Apr 16, 2019 at 3:10 PM Greve, Douglas N.,Ph.D. > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > > > 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> > > <mailto: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>> > > > <mailto: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>> > > > <mailto: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>> > > > <mailto: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> > > <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
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