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Code Block
find $PIPELINEPATH -name tmp -type d -exec rm -rf \{} \;
for file in *_processed/*/resampled/*{__concat_lsq6_N_I_lsq6_lsq12_and_nlin-resampled.mnc,_N_I_lsq6_avg_lsq12-resampled.mnc}; do if [ -f $file ]; then rm -f $file; fi; done \
for file in *_processed/*/transforms/*{_mt_to_,_N_I_lsq6_lsq12_and_nlin_inverted,__concat_lsq6_N_I_lsq6_lsq12_and_nlin}*; do if [ -f $file ]; then rm -f $file; fi; done \
for file in *_processed/*/transforms/*N_I_lsq6_lsq12_and_nlin__concat_inverted_linear_part*; do if [ -f $file ]; then rm -f $file; fi; done
for file in *_processed/*/masking/transforms \/*{mt_to_Dorr_2008_Steadman_2013_Ullmann_2013_on_NRXN1a_v1_average_lsq12,mt_to_Dorr_2008_Steadman_2013_Ullmann_2013_on_NRXN1a_v1_average_nlin_5}*; do if [ -f $file ]; then rm -f $file; fi; done

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Code Block
languagebash
#
# *_processed/*/transforms
#
# From all the transformations that are produced you only need to keep the:
# "inverse pure non linear" - used to calculate relative Jacobians
# "with additional inverted" - used to calculate absolute Jacobians
# "final nlin" - forward transformation that can be used to resample native files to final-nlin space
# the following can all safely be removed:
for file in *_processed/*/transforms/*{-final-nlin_inverse_grid_0.mnc,-final-nlin_inverse.xfm,-final-nlin_with_additional_grid_0.mnc,-final-nlin_with_additional.xfm,-final-nlin_inverted_grid_0.mnc,-final-nlin_inverted.xfm}; do if [ -f $file ]; then rm -f $file; fi; done 

 


Other cleaning:

Once your files are reconned/dist corrected, you can delete the original fid files. You can also delete the phase calibration folder, but given the small size of the procpar and global files, it's worth it to keep them in case we need them in the future.

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Once your data has been published, there's only three files you should be keeping for each subject: the final resampled nlin, the absolute jacobians, and the relative jacobians. You should also keep your atlas. You can delete everything else registration-related.