...
| Code Block |
|---|
# Using the output from the command above you can run the following which only prints all the tmp directories:
> find /path/to/pipeline_processed -name tmp -type d
# and actually remove them
> find /path/to/pipeline_processed -name tmp -type d -exec rm -rfrfv \{} \; |
Another way to find all possible pipeline tmp files and delete them:
| Code Block |
|---|
# remove all possible tmp directories:
> find /main/path/ -path '*_processed/*/tmp' -type d -exec rm -rfrfv \{} \;
# on HPF, that could be one of the following:
> find /hpf/largeprojects/MICe/yourusername/ -path '*_processed/*/tmp' -type d -exec rm -rfrfv \{} \; |
Deep Cleaning
| Code Block |
|---|
|
#
# *_processed/*/resampled
# if you only want to keep the lsq6 and final nlin file:
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 -ffv $file; fi; done |
| Code Block |
|---|
|
#
# *_processed/*/transforms
# From all the transformations that are produced you only need to keep the:
# pure non linear ("*N_I_lsq6_lsq12_and_nlin__concat_inverted_linear_part.xfm") - used to calculate relative Jacobians
# full linear and non linear ("*_N_I_lsq6_lsq12_and_nlin") - used to calculate absolute Jacobians
# the following can all safely be removed:
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 -ffv $file; fi; done
# And if you want to remove the transforms used to create relative jacobians
for file in *_processed/*/transforms/*N_I_lsq6_lsq12_and_nlin__concat_inverted_linear_part*; do if [ -f $file ]; then rm -ffv $file; fi; done |
| Code Block |
|---|
#
# *_processed/*/masking/transforms
# This removes all the transforms used to register to the atlas for initial masking purposes
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 -ffv $file; fi; done |
Other cleaning:
...