new atlas labels created if subject GM voxel undefined in reference parcellation

[shen4brains]

This is a behaviour of AFNI's 3dROIMaker that we need to account for. From the 3dROIMaker documentation (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dROIMaker.html):

If an INSET ROI has no corresponding REFSET label, then the former is marked with an integer greater than the max refset label.

Affected code blocks here: https://github.com/McIntosh-Lab-RRI/tvb-ukbb/blob/3cebec9f0d26ddfb75b82ea7b5ae678a770eb505/bb_structural_pipeline/bb_struct_init#L295 and here: https://github.com/McIntosh-Lab-RRI/tvb-ukbb/blob/3cebec9f0d26ddfb75b82ea7b5ae678a770eb505/bb_diffusion_pipeline/bb_probtrackx2/bb_pre_probtrackx2#L26

Solution:

• use fslmaths to detect max integer label of reference image (refset)
• then use that integer with fslmaths to threshold labelled image output of 3dROImaker

[shen4brains]

• [x] also add -dump_no_labtab flag to 3dROImaker command to prevent label table files from being generated

[shen4brains]

adding here that this issue does not affect fc.txt or sc.txt outputs because the labels for those are chosen from the LUT but correcting the parcellation images will enable accurate future use of the images