Hi there,

 

I am running into a problem when using qatools.py to qa my recon-all. Some of my participants process ok, but with others I get the error below. Any advice on what to do to address this?

 

Many thanks,

Elizabeth

 

ERROR:

 

Computing white and gray matter SNR for orig.mgz ...

Traceback (most recent call last):

  File "/Applications/freesurfer_v7.1.0/python/scripts/qatools.py", line 17, in <module>

    qatoolspython.run_qatools(subjects_dir, output_dir, subjects, shape, screenshots, fornix, outlier, outlier_table)

  File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/qatoolspython.py", line 883, in run_qatools

    _do_qatools(subjects_dir, output_dir, subjects, shape, screenshots, fornix, outlier, outlier_table)

  File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/qatoolspython.py", line 663, in _do_qatools

    wm_snr_orig, gm_snr_orig = checkSNR(subjects_dir, subject, SNR_AMOUT_EROSION, ref_image="orig.mgz")

  File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/checkSNR.py", line 83, in checkSNR

    b_wm_data[x,y,z] = 1

IndexError: index 256 is out of bounds for axis 2 with size 256