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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
> >     >     >>
> >     >     >>
> >     >     >>
> >     >     >>  _______________________________________________
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> >     >     <mailto:Freesurfer@nmr.mgh.harvard.edu
> >     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> >     >     >>
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