Labelconvert problems with surface-based parcellations after FreeSurfer update (>=7.1.0)

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Hi!

I noticed that after updating my FreeSurfer to version 7.1.0, labelconvert yields problems when applied with surface-based parcellations. For example, the following command

labelconvert aparc+aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt $HOME/mrtrix3/share/mrtrix3/labelconvert/fs_default.txt dk_parcels.mif

produces a warning, saying that nodes 36 and 43 are missing from the parcellation. These nodes correspond to the left and right thalami. It seems the reason for this warning is that FreeSurfer has changed some naming conventions in the lookup table in the new release. One of the changes is that previously, the thalamus was referred to as “Thalamus-Proper”. This is no longer the case. However, the fs_default.txt lookup table that comes with MRtrix3 still has that “old” naming convention. This issue can be easily fixed when modifying the thalamus labels in the fs_default.txt lookup table from “Left-Thalamus-Proper” (ID 36)/”Right-Thalamus-Proper” (ID 43) to “Left-Thalamus” and “Right-Thalamus”. After that, labelconvert worked fine for me. Maybe this helps others as well, encountering a similar problem!

Cheers,
Marlene

1 Like
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Thanks for the heads up. I have also had problems with labelconvert lately because when I re-installed Freesurfer the FreeSurferColorLUT.txt file was missing left and right insula, so I had to add them manually to make the DK atlas work.

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Hi Graham. Hm, weird, in my version of the FreeSurferColorLUT.txt the left and right insulae are not missing. Do you have FreeSurfer 7.0 or >7.1.0 installed?

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Hi Marlene,

After taking a second look at this, I figured out that when the left and right insula (index 1035 and 2035) were missing from FreeSurferColorLUT.txt, I had actually just pulled the file from this link: https://github.com/INCF/XCEDE/blob/master/examples/volumetric/FreeSurferColorLUT.txt

I think I was just being lazy when making a new pipeline and needed the file for an MRTrix3 ‘labelconvert’ step, but didn’t want to re-install all of FreeSurfer.

I only figured out that the file was bad after my parcellations kept missing the left and right insula.

So I guess the lesson is to be careful where you get the FreeSurferColorLUT.txt file - seem to be slightly different versions floating around.

Graham

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Hi Marlene,

The issue was reported previously and was resolved in version 3.0.1 and reported in the changelog. So hopefully just doing a macro version update should resolve the issue without necessitating manual editing of files locally.

So I guess the lesson is to be careful where you get the FreeSurferColorLUT.txt file - seem to be slightly different versions floating around.

Yes, I’ve observed the same myself also. But it was recently pointed out to me that the FreeSurfer code is now on GitHub, which means that e.g. you could download the LUT for any version tag of interest directly.

Rob