Hello!

I encountered 3 issues with recon_all_clinical:

1. Both version 7.4.0 and version 7.4.1 do not generate aseg.stat file. Is this normal? I would like to extract volume parcellations via asegstats2table given that I need the volume parcellations as typically presented in aseg.stat. Is there a way to extract aseg.stat from aseg.mgz or another solution to extract aseg.stat volumes?
2. Version 7.4.0 throws errors at the end of the script (even with the replacement file). “ERROR: cannot find or read /cluster/project7/brain_age/software/freesurfer-7.4.0/freesurfer/average/colortable_BA_thresh.txt” and “ERROR: cannot find or read /cluster/project7/brain_age/software/freesurfer-7.4.0/freesurfer/average/colortable_BA_thresh.txt.” I checked, “colortable_BA.txt” exists but “colortable_BA_thresh.txt” doesn’t. If I rename the latter file to “colortable_BA_thresh.txt”, then it fixes the errors. Is this the correct way to address the problem?
3. Version 7.4.1 has a similar error as above, but it seems to be due to the incorrect path: ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt.

Any help, particularly with problem 1, would be much appreciated!

Thank you,

Fran

 

Francesca Biondo, PhD | Senior Research Fellow | Centre for Medical Image Computing | Computer Science | UCL | f.biondo@ucl.ac.uk