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> 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
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