Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

🚧 Makefile: no bulk rename of original dcm, _ - important for reproin name #5

Open
wants to merge 1 commit into
base: makeFile
Choose a base branch
from
Open

🚧 Makefile: no bulk rename of original dcm, _ - important for reproin name #5

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 15 additions & 9 deletions Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,22 +11,28 @@ examples/dicom/6/: examples/
wget https://github.com/user-attachments/files/15515915/gre_phantom_dcm_nii.zip
unzip gre_phantom_dcm_nii.zip
cd dicom/
mkdir 5
mkdir 6
mkdir 5 6
mv TESTBR.MR.DEV-SCHIRDA_041119_BRAINO.0005.* 5
mv TESTBR.MR.DEV-SCHIRDA_041119_BRAINO.0006.* 6

.venv/bin/activate:
./setup_env.bash

# want to rename each dicom's acquistion name stored in the header
# will match reproin format (BIDS-like)
# ISSUE: one scanner sequence produces two folders. one should be fmap-mag the other fmap-phase
# but can only set one name (at the scanner). so leave off the '-mag' or '-phase'
.ONESHELL:
dcm-rehead/: examples/dicom/6/ | .venv/bin/activate
. .venv/bin/activate && \
rename 's/-//g' examples/dicom/5/* && \
rename 's/_//g' examples/dicom/5/* && \
rename 's/-//g' examples/dicom/6/* && \
rename 's/_//g' examples/dicom/6/* && \
dicom-rewrite-pname -o dcm-rehead//5 -n fmapacqdwi examples/dicom/5/* && \
dicom-rewrite-pname -o dcm-rehead//6 -n fmapacqdwi examples/dicom/6/*
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

fromfmapacqdwi to reproin/bids-like fmap_acq-dwi

# rename 's/[-_]//g' examples/dicom/[56]/*
# NB!! why kill the - and _ separaters in the original files?
# probably don't want to touch these
# we are only testing what happens if we change the dicom acq. seq. name
# we can't control the actual output file names
#
. .venv/bin/activate
dicom-rewrite-pname -o dcm-rehead/5 -n fmap_acq-dwi examples/dicom/5/*
dicom-rewrite-pname -o dcm-rehead/6 -n fmap_acq-dwi examples/dicom/6/*

txt/input-reproin.txt: dcm-rehead/ $(wildcard dcm-rehead/*)
dcmdirtab -d 'dcm-rehead/*' > $@
Expand Down