Boney Main Issues

[robdahn]

Create main SPM12 toolbox with:

• [ ] toolbox configuration file (including test for CAT12)
• [x] main bone processing batch
• [ ] HTML overview with basic information as some poster-like X-bone design
• [ ] example batch (that uses some images delivered by SPM/CAT or nice public examples)

[PolonaCa]

Processing Issues:

• [ ] XML2CSV batch with the "export fields setting" is not working correctly. Export is only including 44 files in all cases except the "Detailed" setting. An option to export everything would be required for experts.
• [ ] Check the use of "boneyPPmat_*.mat" for CAT/SPM. Think also about to include the preprocessing method in the filenames.
• [ ] Command line report for default users with confusing warnings (should not appear in the short cmd report and only in the verbose mode 2). Moreover, the warning should be only a note as the SPM segments were corrected.

  2931)           ./MRData/202301_MRIbones/ukb_bones/sub-5996501_ses-2_T1w.nii,1:    T1w    low   high   1.00   0.01 |   2.42   5.53   8.29   8.82    NaN |   3.00   1.81   7.43   8.19    NaN |   0.12   1.29   0.43   2.00  46s  1W
  ------------------------------------------------------------------------
   WARNING 01:  boney_segment_evalSPMseg:badSPMcls4
                Bad SPM tissue class 4 - probably underestimated (0.39)
  ------------------------------------------------------------------------
  2932)           ./MRData/202301_MRIbones/ukb_bones/sub-5996641_ses-2_T1w.nii,1:    T1w    low   high   1.00   0.01 |   2.09   2.54   6.88   9.02    NaN |   1.85   0.91   5.63   8.19    NaN |   0.08   0.58   0.40   0.96  44s  1W

• [ ] Check variables with NaNs in command line report (maybe it is the BMDH variable?):

  2931)           ./MRData/202301_MRIbones/ukb_bones/sub-5996501_ses-2_T1w.nii,1:    T1w    low   high   1.00   0.01 |   2.42    2932)           ./MRData/202301_MRIbones/ukb_bones/sub-5996641_ses-2_T1w.nii,1:    T1w    low   high   1.00   0.01 |   2.09   2.54   6.88   9.02    NaN |   1.85   0.91   5.63   8.19    NaN |   0.08   0.58   0.40   0.96  44s  1W