On Tue, Apr 16, 2019 at 3:10 PM Greve, Douglas N.,Ph.D. <DGREVE@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.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@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.
> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@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
> >>
> >>
> >>
> >> _______________________________________________
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