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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> 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>> 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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