[labelconvert] bilateral thalamus gone

preprocessing

#1

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??

Best,
Jiook


#2

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

:man_shrugging:

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.

Rob


#3

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.

Regarding:

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

Cheers.
Jimmy