-add-seg-only flag should be moved to copy_files_to_derivatives.py

[valosekj]

Currently, the -add-seg-only flag is available within manual_correction.py script:

manual-correction/manual_correction.py

Lines 197 to 199 in 10ed254

	'-add-seg-only',
	help="Only copy the source files (segmentation) that aren't in -config list to the 'derivatives' folder. "
	"Use this flag to add manually QC-ed automatic segmentations to the 'derivatives' folder.",

But it would make sense to move this flag to copy_files_to_derivatives.py.

[valosekj]

Also, `add-seg-only` works only for SC and GM seg and not for disc labels:

manual-correction/manual_correction.py

Lines 624 to 625 in 10ed254

	if task in ['FILES_SEG', 'FILES_GMSEG']:
	if not args.add_seg_only:

For record purposes, I used the following command to copy automatically generated labels to git-annex dataset:

for sub in sub*;do cd ${sub}/anat;if [[ ! -f ~/extrassd1/janvalosek/data/dcm-zurich/derivatives/labels/${sub}/anat/${sub}_acq-sagittal_T2w_labels-manual.nii.gz ]];then cp ${sub}_acq-sagittal_T2w_label-SC_mask_labeled_discs.nii.gz ~/extrassd1/janvalosek/data/dcm-zurich/derivatives/labels/${sub}/anat/${sub}_acq-sagittal_T2w_labels-manual.nii.gz;fi;cd ../..;done

And the following command to create dummy json sidecars:

for sub in sub*;do cd ${sub}/anat; if [[ -f ${sub}_acq-sagittal_T2w_labels-manual.nii.gz && ! -f ${sub}_acq-sagittal_T2w_labels-manual.json ]];then; touch ${sub}_acq-sagittal_T2w_labels-manual.json;fi;cd ../..;done

UPDATE: we store only manually created disc labels under derivatives, context here