Added output file and/or folder flag (#2264)
Added output file and/or folder flag (#2264)

* sct_compute_mtr: Add flag to set output filename and location (fixes #2178)

* sct_compute_mtr: fixed case where fsleyes command would not open output file if its location had changed (fixes #2178)

* sct_compute_mtr: fixed formatting of code and comments (fixes #2178)

* sct_compute_mtr: removed undefined variable 'param' when defining flag '-omtr' (fixes #2178)

* sct_compute_mtr: redefined '-omtr' to '-o'  to respect conventions (fixes #2178)

* sct_compute_mtr: changed description for '-o' by specifying to add extension '.nii.gz'. (fixes #2178)

* sct_compute_mtr: changed example for '-o' argument for a more concrete one (fixes #2178)

* sct_compute_mtr: added extension to default value for '-o' argument (fixes #2178)

* sct_compute_mtr: removed addition of extension of file to prevent it being present twice in a row in output name (fixes #2178)

* sct_compute_mtr: removed notification about moving location before using command 'fsleyes'(fixes #2178)

* sct_compute_mtr: moved shutil import to the top (fixes #2178)

* sct_compute_mtr: removed ".nii.gz" when specifying extension in description of argument '-o' (fixes #2178)

* sct_compute_mtr: modified code to respect convention of file_out not including extension.

* sct_compute_mtr: removed temporary folder steps and simplified argument variables

* sct_compute_mtr: fixed case where outputting a .nii.gz file would fail

* sct_compute_mtr: removed steps where mt0.nii and mt1.nii would be copied

* sct_compute_mtr: fixed case where mt0 and mt1 files were not set to predetermined values

* sct_compute_mtr: removed variables ext_out and file_out

* sct_compute_mtr: fixed case where fsleyes viewing command could not be issued from cwd

* sct_compute_mtr: removed remnant step from temporary folder process

* sct_compute_mtr: removed redundant generate_output_file step

* sct_compute_mtr: removed '-r' argument in get_parser()


Former-commit-id: a1aae053e6669cbb1870ad4dc478b185af6e676c
neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox,neuropoly/spinalcordtoolbox