Labelconvert error

1

Hi all,

I’m encountering an issue when running MRtrix3’s 5ttgen freesurfer command. During processing, the labelconvert step throws the following error:

[ERROR] Inconsistent number of columns in LUT file "FreeSurferColorLUT.txt"
[ERROR] Initial file contents contain 6 columns, but line 511 contains 7 entries:
[ERROR] "819 Left-HypoThal-noMB           0  80   0 0 2"

Upon inspecting the FreeSurferColorLUT.txt file, I noticed that some lines (e.g., below) contain 7 columns instead of the expected 6:

# sclimbic
819 Left-HypoThal-noMB           0  80   0 0 2
820 Right-HypoThal-noMB         15 165   15 0 2
821 Left-Fornix                  0 255 255 0 3
822 Right-Fornix                27 187 253 0 3 
843 Left-MammillaryBody        178 255  80 0 2
844 Right-MammillaryBody        25 246  80 0 2
853 Mid-AntCom                  60  58 210 0 3
865 Left-Basal-Forebrain       170  85   0 0 2
866 Right-Basal-Forebrain      139  69  19 0 2
869 Left-SeptalNuc             255 170 255 0 2
870 Right-SeptalNuc            191 127 191 0 2
...

Could someone please advise how to handle or fix this 7-column format so that labelconvert runs correctly? Any recommended solutions or workarounds would be greatly appreciated!

Thanks in advance!

2

Hi Maiwulanjiang,
Welcome to the forum!

This has been flagged by Freesurfer (see here for details).

A quick fix would be to remove the last column containing the 2s and 3s from the LUT

Hope this helps :slight_smile:
Arkiev

3

Thanks a lot, adsouza! That fix did the trick—removing the last column solved the issue. Really appreciate your help!

Cheers,
Maiwulanjiang

1 Like