[labelconvert] bilateral thalamus gone



Hi Rob,

In my group analysis (N=~200), I found that labelconvert “skipped” specifically the bilateral thalamus. No error messages until I ran tck2connectome:

tck2connectome: [WARNING] existing output files will be overwritten
tck2connectome: [WARNING] The following nodes are missing from the parcellation image:
tck2connectome: [WARNING] 76, 83
tck2connectome: [WARNING] (This may indicate poor parcellation image preparation, use of incorrect or incomplete LUT file(s) in labelconvert, or very poor registration)

Please find this figure showing the original freesurfer aparc+aseg (greyscale) overlaid with the “converted” aparc+aseg (yellow-red), which does not include the thalamus.

I used FreeSurferColotLUT.txt containing:

49 Right-Thalamus-Proper

and mrtrix’s fs_default.txt containing:

43 R.TH Right-Thalamus-Proper

Why would this error occur only to the thalamus across all subjects??



Why would this error occur only to the thalamus across all subjects?


Never seen this before…

Only thing I can suggest is checking the raw image intensity within the thalami of the input image to labelconvert i.e. the raw FreeSurfer output: maybe they have been labelled by FreeSurfer as e.g. “Right-Thalamus” (48) instead of “Right-Thalamus-Proper” (49)?

This issue can crop up with custom lookup tables due to minor spelling errors: The name of the node must be precisely identical between the two lookup tables in order for labelconvert to construct the input-output index mapping. But given you’re using software-provided lookup table files as both input and output, I wouldn’t expect this to have occurred in your case.



Hi @Jiook_Cha,

According to this line, I guess you actually used fs_a2009s.txt for the lut_out argument when running labelconvert? In this case, the input parcellation image needs to be aparc.a2009s+aseg.mgz as provided by FreeSurfer, not the aparc+aseg as you described.

But having said that you also mentioned:

So, I would suggest that you check your labelconvert step to ensure the consistency of your inputs.


No, that has not been changed with the latest FreeSurfer (v6.0).