From c207c9e388fe787d9d5ce6d944bc1fd68ccc1a78 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:19:11 -0400 Subject: [PATCH 01/18] Create pip-delete-this-directory.txt --- docker/src/pip-delete-this-directory.txt | 1 + 1 file changed, 1 insertion(+) create mode 100644 docker/src/pip-delete-this-directory.txt diff --git a/docker/src/pip-delete-this-directory.txt b/docker/src/pip-delete-this-directory.txt new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/docker/src/pip-delete-this-directory.txt @@ -0,0 +1 @@ + From e36d9c0eb6ffc0fd501a35eb48af204ef2a7f586 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:19:52 -0400 Subject: [PATCH 02/18] Create README --- docker/src/eddy-qc/README | 1 + 1 file changed, 1 insertion(+) create mode 100644 docker/src/eddy-qc/README diff --git a/docker/src/eddy-qc/README b/docker/src/eddy-qc/README new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/docker/src/eddy-qc/README @@ -0,0 +1 @@ + From 60b8dc14ab7c087bee14378eb3e4eb79605da6fb Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:20:41 -0400 Subject: [PATCH 03/18] eddy-qc files for distortion correction --- docker/src/eddy-qc/README | 107 ++++++++++++++++++++++++++++ docker/src/eddy-qc/requirements.txt | 5 ++ docker/src/eddy-qc/setup.py | 11 +++ 3 files changed, 123 insertions(+) create mode 100644 docker/src/eddy-qc/requirements.txt create mode 100644 docker/src/eddy-qc/setup.py diff --git a/docker/src/eddy-qc/README b/docker/src/eddy-qc/README index 8b13789..aa8ace2 100644 --- a/docker/src/eddy-qc/README +++ b/docker/src/eddy-qc/README @@ -1 +1,108 @@ +------------------------------------------- +EDDY QC +Matteo Bastiani, FMRIB +August, 2017 +------------------------------------------- +Automated tools based on FSL's eddy to perform quality assessment on diffusion mri (dMRI) datasets. +Installation +------------ +The eddy qc tools will be distributed with FSL. + +If you want to install the tools within your python (>= 3.5) environment, once the library has been downloaded, run: +cd /path-to-lib/eddy_qc +python setup.py install + +Wiki page +--------- +https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddyqc + + +------------------------------------------- +QUAD (QUality Assessment for DMRI) +------------------------------------------- +Generates a QC report pdf and stores the QC indices in a .json file for single subject dMRI data. + +The script will look for eddy output files that have been generated according to the user-specified options. If a feature, e.g., output the CNR maps, has not been used, then no CNR page will be added to the final report. +The script also produces a qc.json file that contains summery qc indices and basic information about the data. The JSON file can then be read by SQUAD to generate a group report. + +Compulsory arguments: + eddyBase Basename (including path) specified when running EDDY + -idx, --eddyIdx File containing indices for all volumes into acquisition parameters + -par, --eddyParams File containing acquisition parameters + -m, --mask Binary mask file + -b, --bvals b-values file + +Optional arguments: + -g, --bvecs b-vectors file - only used when .eddy_residuals file is present + -o, --output-dir Output directory - default = '.qc' + -f, --field TOPUP estimated field (in Hz) + -s, -slspec Text file containing acquisition details + -v, --verbose Display debug messages + +Output: + output-dir/qc.pdf: single subject QC report + output-dir/qc.json: single subject QC and data info database + output-dir/vols_no_outliers.txt: text file that contains the list of the non-outlier volumes (based on eddy residuals) + +Examples +-------- +cd folder-where-eddy-output-is +Assuming eddy basename is "eddy_corrected" + +Minimal running style: + eddy_quad eddy_corrected -idx eddyIndex.txt -par acqparams.txt -m nodif_brain_mask.nii.gz -b bvals + This will make a eddy_corrected.qc folder, where qc.pdf and qc.json will be stored. +Complete running style: + eddy_quad eddy_corrected -idx eddyIndex.txt -par acqparams.txt -m nodif_brain_mask.nii.gz -b bvals -g bvecs -f fieldmap.nii.gz -o qc_output_dir + This will make a qc_output_dir folder, where qc.pdf and qc.json will be stored. As bvecs were specified, the tool will also generate "clean" (i.e., outliers free) bvecs and bvals files, based on the eddy_residuals. A voxel displacement map will be obtained using the provided fieldmap (in Hz) and the standard deviation of the voxel displacement within the masked volume will be stored. + +To clean the dataset, i.e., removing the outliers, run: +fslselectvols -i eddy_corrected -o eddy_corrected_clean --vols=qc_output_dir/vols_no_outliers.txt + + +------------------------------------------- +SQUAD (Study-wise QUality Assessment for DMRI) +------------------------------------------- +Generates a QC report pdf and database for whole-study dMRI data. +Updates single subject's report based on the study-specific database or using a previously generated one from a different study. +Groups the distributions of the QC indices based on a user-specified grouping variable. + +The script will look for QUAD .json output files that are generated at the locations specified by the user in a text file. + +Compulsory arguments: + list Text file containing a list of squad qc folders + +Optional arguments: + -g, --grouping Text file containing grouping variable for the listed subjects + -u, --update [group_db.json] Update existing eddy_squad reports after generating group report or using a pre-existing [group_db.json] one + -gdb, --group-db Text file containing grouping variable for the database subjects + -o, --output-dir Output directory - default = '.qc' + +Output: + output-dir/group_qc.pdf: study-wise QC report + output-dir/group_db.json: study-wise QC database + +Examples +-------- +Assuming qc_folders.txt file is structured as: +subj1/eddy_corrected.qc +subj2/eddy_corrected.qc +subj3/eddy_corrected.qc +... +and group.txt file is structured as (first row is the label): +Group +1 +0 +1 +... + +Minimal running style: + eddy_squad qc_folders.txt + This will generate a quad directory where group_db.json (database) and group_qc.pdf (report) will be stored. +Complete running style: + eddy_squad qc_folders.txt -u -g group.txt -o quad_group + This will generate a quad_group directory where group_db.json (database) and group_qc.pdf (report) will be stored. Individual subjects' QC reports previously generated by QUAD will be updated by adding extra pages that will show the single sunject in the context of the study and marking QC indices as outliers in the tables where needed. Extra pages will be added to the report where distributions for individual QC indices will account for the specified grouping variable. +Using a previously generated database: + eddy_squad qc_folders.txt -u study/group_db.json -g group.txt -gdb group_db.txt -o quad_group + Same as before, but this time we are using a previously generated database to update the single subject reports. !!!NB!!! If using a grouping variable, it is required to specify the same grouping variable for the subjects of the previously generated database as a different variable. diff --git a/docker/src/eddy-qc/requirements.txt b/docker/src/eddy-qc/requirements.txt new file mode 100644 index 0000000..f320138 --- /dev/null +++ b/docker/src/eddy-qc/requirements.txt @@ -0,0 +1,5 @@ +nibabel==2.* +scipy +matplotlib +seaborn +PyPDF2 diff --git a/docker/src/eddy-qc/setup.py b/docker/src/eddy-qc/setup.py new file mode 100644 index 0000000..625627c --- /dev/null +++ b/docker/src/eddy-qc/setup.py @@ -0,0 +1,11 @@ +from setuptools import setup,find_packages +with open('requirements.txt', 'rt') as f: + install_requires = [l.strip() for l in f.readlines()] + +setup(name='eddy_qc', + version='1.0.0', + description='EDDY Quality Control tools', + author='Matteo Bastiani', + install_requires=install_requires, + scripts=['eddy_qc/scripts/eddy_squad','eddy_qc/scripts/eddy_quad'], + packages=find_packages()) From 15c61cdce8be72923f777cddf3f0e52a1ced74f5 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:21:43 -0400 Subject: [PATCH 04/18] added by pip --- docker/src/pip-delete-this-directory.txt | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docker/src/pip-delete-this-directory.txt b/docker/src/pip-delete-this-directory.txt index 8b13789..c8883ea 100644 --- a/docker/src/pip-delete-this-directory.txt +++ b/docker/src/pip-delete-this-directory.txt @@ -1 +1,5 @@ +This file is placed here by pip to indicate the source was put +here by pip. +Once this package is successfully installed this source code will be +deleted (unless you remove this file). From 25b07ebfcc9a0d7a5de96d6237e20011b009b873 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:33:24 -0400 Subject: [PATCH 05/18] Create condaRecipes --- docker/src/eddy-qc/condaRecipes | 1 + 1 file changed, 1 insertion(+) create mode 100644 docker/src/eddy-qc/condaRecipes diff --git a/docker/src/eddy-qc/condaRecipes b/docker/src/eddy-qc/condaRecipes new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/docker/src/eddy-qc/condaRecipes @@ -0,0 +1 @@ + From 0b0adffee79d0574d17520b85fb68293af209d1c Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:35:04 -0400 Subject: [PATCH 06/18] delete condaRecipes --- docker/src/eddy-qc/condaRecipes | 1 - 1 file changed, 1 deletion(-) delete mode 100644 docker/src/eddy-qc/condaRecipes diff --git a/docker/src/eddy-qc/condaRecipes b/docker/src/eddy-qc/condaRecipes deleted file mode 100644 index 8b13789..0000000 --- a/docker/src/eddy-qc/condaRecipes +++ /dev/null @@ -1 +0,0 @@ - From 8d02fa3adf5cd71735a0846c520c6f1d781bc7e2 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:35:45 -0400 Subject: [PATCH 07/18] Create meta.yml --- docker/src/eddy-qc/condaRecipes/meta.yml | 1 + 1 file changed, 1 insertion(+) create mode 100644 docker/src/eddy-qc/condaRecipes/meta.yml diff --git a/docker/src/eddy-qc/condaRecipes/meta.yml b/docker/src/eddy-qc/condaRecipes/meta.yml new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/docker/src/eddy-qc/condaRecipes/meta.yml @@ -0,0 +1 @@ + From 6c55f3d7c03cdd55e4e17340ac9a7e550a448038 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:36:15 -0400 Subject: [PATCH 08/18] added missing files in condaRecipes --- docker/src/eddy-qc/condaRecipes/meta.yaml | 44 +++++++++++++++++++ docker/src/eddy-qc/condaRecipes/post-link.sh | 3 ++ docker/src/eddy-qc/condaRecipes/pre-unlink.sh | 3 ++ 3 files changed, 50 insertions(+) create mode 100644 docker/src/eddy-qc/condaRecipes/meta.yaml create mode 100644 docker/src/eddy-qc/condaRecipes/post-link.sh create mode 100644 docker/src/eddy-qc/condaRecipes/pre-unlink.sh diff --git a/docker/src/eddy-qc/condaRecipes/meta.yaml b/docker/src/eddy-qc/condaRecipes/meta.yaml new file mode 100644 index 0000000..0206718 --- /dev/null +++ b/docker/src/eddy-qc/condaRecipes/meta.yaml @@ -0,0 +1,44 @@ +{% set data = load_setup_py_data() %} +package: + name: eddy_qc + version: {{ data['version']}} + +build: + noarch: python + script: python setup.py install --single-version-externally-managed --record=record.txt + +source: + path: ../ + +requirements: + build: + - python >2 + - setuptools + {% for package in data.get('setup_requires', {}) %} + - {{ package.lower() }} + {% endfor %} + + run: + - python >2 + {% for package in data.get('install_requires', {}) %} + - {{ package.lower() }} + {% endfor %} + + run_constrained: + {% for name, pkgs in data.get('extras_require', dict()).items() %} + {% for package in pkgs %} + - {{ package.lower() }} + {% endfor %} + {% endfor %} + +{% if 'test_suite' in data %} +test: + requires: + {% for package in data.get('setup_requires', {}) %} + - {{ package.lower() }} + {% endfor %} + source_files: + - {{ data['test_suite'] }} + commands: + - python -m pytest {{ data['test_suite'] }} +{% endif %} diff --git a/docker/src/eddy-qc/condaRecipes/post-link.sh b/docker/src/eddy-qc/condaRecipes/post-link.sh new file mode 100644 index 0000000..1827263 --- /dev/null +++ b/docker/src/eddy-qc/condaRecipes/post-link.sh @@ -0,0 +1,3 @@ +if [ -e ${FSLDIR}/etc/fslconf/requestFSLpythonLink.sh ]; then + $FSLDIR/etc/fslconf/requestFSLpythonLink.sh eddy_squad eddy_quad +fi diff --git a/docker/src/eddy-qc/condaRecipes/pre-unlink.sh b/docker/src/eddy-qc/condaRecipes/pre-unlink.sh new file mode 100644 index 0000000..fac65eb --- /dev/null +++ b/docker/src/eddy-qc/condaRecipes/pre-unlink.sh @@ -0,0 +1,3 @@ +if [ -e ${FSLDIR}/etc/fslconf/requestFSLpythonUnlink.sh ]; then + $FSLDIR/etc/fslconf/requestFSLpythonUnlink.sh eddy_squad eddy_quad +fi From b8e75a6036d1dc66c35af23d673e0bbc33e2765a Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:45:16 -0400 Subject: [PATCH 09/18] Delete meta.yaml --- docker/src/eddy-qc/condaRecipes/meta.yaml | 44 ----------------------- 1 file changed, 44 deletions(-) delete mode 100644 docker/src/eddy-qc/condaRecipes/meta.yaml diff --git a/docker/src/eddy-qc/condaRecipes/meta.yaml b/docker/src/eddy-qc/condaRecipes/meta.yaml deleted file mode 100644 index 0206718..0000000 --- a/docker/src/eddy-qc/condaRecipes/meta.yaml +++ /dev/null @@ -1,44 +0,0 @@ -{% set data = load_setup_py_data() %} -package: - name: eddy_qc - version: {{ data['version']}} - -build: - noarch: python - script: python setup.py install --single-version-externally-managed --record=record.txt - -source: - path: ../ - -requirements: - build: - - python >2 - - setuptools - {% for package in data.get('setup_requires', {}) %} - - {{ package.lower() }} - {% endfor %} - - run: - - python >2 - {% for package in data.get('install_requires', {}) %} - - {{ package.lower() }} - {% endfor %} - - run_constrained: - {% for name, pkgs in data.get('extras_require', dict()).items() %} - {% for package in pkgs %} - - {{ package.lower() }} - {% endfor %} - {% endfor %} - -{% if 'test_suite' in data %} -test: - requires: - {% for package in data.get('setup_requires', {}) %} - - {{ package.lower() }} - {% endfor %} - source_files: - - {{ data['test_suite'] }} - commands: - - python -m pytest {{ data['test_suite'] }} -{% endif %} From 8613bd0e26f6e0708bf85305861d7aa433a0fe45 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:45:28 -0400 Subject: [PATCH 10/18] Delete meta.yml --- docker/src/eddy-qc/condaRecipes/meta.yml | 1 - 1 file changed, 1 deletion(-) delete mode 100644 docker/src/eddy-qc/condaRecipes/meta.yml diff --git a/docker/src/eddy-qc/condaRecipes/meta.yml b/docker/src/eddy-qc/condaRecipes/meta.yml deleted file mode 100644 index 8b13789..0000000 --- a/docker/src/eddy-qc/condaRecipes/meta.yml +++ /dev/null @@ -1 +0,0 @@ - From 34a03fea312728ac7ef57aab78411bd72d080a58 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:45:37 -0400 Subject: [PATCH 11/18] Delete post-link.sh --- docker/src/eddy-qc/condaRecipes/post-link.sh | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 docker/src/eddy-qc/condaRecipes/post-link.sh diff --git a/docker/src/eddy-qc/condaRecipes/post-link.sh b/docker/src/eddy-qc/condaRecipes/post-link.sh deleted file mode 100644 index 1827263..0000000 --- a/docker/src/eddy-qc/condaRecipes/post-link.sh +++ /dev/null @@ -1,3 +0,0 @@ -if [ -e ${FSLDIR}/etc/fslconf/requestFSLpythonLink.sh ]; then - $FSLDIR/etc/fslconf/requestFSLpythonLink.sh eddy_squad eddy_quad -fi From 293228d623aba9ffd201e845a91c927e94937ae7 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:45:48 -0400 Subject: [PATCH 12/18] Delete pre-unlink.sh --- docker/src/eddy-qc/condaRecipes/pre-unlink.sh | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 docker/src/eddy-qc/condaRecipes/pre-unlink.sh diff --git a/docker/src/eddy-qc/condaRecipes/pre-unlink.sh b/docker/src/eddy-qc/condaRecipes/pre-unlink.sh deleted file mode 100644 index fac65eb..0000000 --- a/docker/src/eddy-qc/condaRecipes/pre-unlink.sh +++ /dev/null @@ -1,3 +0,0 @@ -if [ -e ${FSLDIR}/etc/fslconf/requestFSLpythonUnlink.sh ]; then - $FSLDIR/etc/fslconf/requestFSLpythonUnlink.sh eddy_squad eddy_quad -fi From 198c81e337f6779e45943251983e957ff2628751 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:46:09 -0400 Subject: [PATCH 13/18] Delete pip-delete-this-directory.txt --- docker/src/pip-delete-this-directory.txt | 5 ----- 1 file changed, 5 deletions(-) delete mode 100644 docker/src/pip-delete-this-directory.txt diff --git a/docker/src/pip-delete-this-directory.txt b/docker/src/pip-delete-this-directory.txt deleted file mode 100644 index c8883ea..0000000 --- a/docker/src/pip-delete-this-directory.txt +++ /dev/null @@ -1,5 +0,0 @@ -This file is placed here by pip to indicate the source was put -here by pip. - -Once this package is successfully installed this source code will be -deleted (unless you remove this file). From 80fd8c76b7ae7c7bda91789fe77aea41b9876c87 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:46:22 -0400 Subject: [PATCH 14/18] Delete README --- docker/src/eddy-qc/README | 108 -------------------------------------- 1 file changed, 108 deletions(-) delete mode 100644 docker/src/eddy-qc/README diff --git a/docker/src/eddy-qc/README b/docker/src/eddy-qc/README deleted file mode 100644 index aa8ace2..0000000 --- a/docker/src/eddy-qc/README +++ /dev/null @@ -1,108 +0,0 @@ -------------------------------------------- -EDDY QC -Matteo Bastiani, FMRIB -August, 2017 -------------------------------------------- -Automated tools based on FSL's eddy to perform quality assessment on diffusion mri (dMRI) datasets. - -Installation ------------- -The eddy qc tools will be distributed with FSL. - -If you want to install the tools within your python (>= 3.5) environment, once the library has been downloaded, run: -cd /path-to-lib/eddy_qc -python setup.py install - -Wiki page ---------- -https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddyqc - - -------------------------------------------- -QUAD (QUality Assessment for DMRI) -------------------------------------------- -Generates a QC report pdf and stores the QC indices in a .json file for single subject dMRI data. - -The script will look for eddy output files that have been generated according to the user-specified options. If a feature, e.g., output the CNR maps, has not been used, then no CNR page will be added to the final report. -The script also produces a qc.json file that contains summery qc indices and basic information about the data. The JSON file can then be read by SQUAD to generate a group report. - -Compulsory arguments: - eddyBase Basename (including path) specified when running EDDY - -idx, --eddyIdx File containing indices for all volumes into acquisition parameters - -par, --eddyParams File containing acquisition parameters - -m, --mask Binary mask file - -b, --bvals b-values file - -Optional arguments: - -g, --bvecs b-vectors file - only used when .eddy_residuals file is present - -o, --output-dir Output directory - default = '.qc' - -f, --field TOPUP estimated field (in Hz) - -s, -slspec Text file containing acquisition details - -v, --verbose Display debug messages - -Output: - output-dir/qc.pdf: single subject QC report - output-dir/qc.json: single subject QC and data info database - output-dir/vols_no_outliers.txt: text file that contains the list of the non-outlier volumes (based on eddy residuals) - -Examples --------- -cd folder-where-eddy-output-is -Assuming eddy basename is "eddy_corrected" - -Minimal running style: - eddy_quad eddy_corrected -idx eddyIndex.txt -par acqparams.txt -m nodif_brain_mask.nii.gz -b bvals - This will make a eddy_corrected.qc folder, where qc.pdf and qc.json will be stored. -Complete running style: - eddy_quad eddy_corrected -idx eddyIndex.txt -par acqparams.txt -m nodif_brain_mask.nii.gz -b bvals -g bvecs -f fieldmap.nii.gz -o qc_output_dir - This will make a qc_output_dir folder, where qc.pdf and qc.json will be stored. As bvecs were specified, the tool will also generate "clean" (i.e., outliers free) bvecs and bvals files, based on the eddy_residuals. A voxel displacement map will be obtained using the provided fieldmap (in Hz) and the standard deviation of the voxel displacement within the masked volume will be stored. - -To clean the dataset, i.e., removing the outliers, run: -fslselectvols -i eddy_corrected -o eddy_corrected_clean --vols=qc_output_dir/vols_no_outliers.txt - - -------------------------------------------- -SQUAD (Study-wise QUality Assessment for DMRI) -------------------------------------------- -Generates a QC report pdf and database for whole-study dMRI data. -Updates single subject's report based on the study-specific database or using a previously generated one from a different study. -Groups the distributions of the QC indices based on a user-specified grouping variable. - -The script will look for QUAD .json output files that are generated at the locations specified by the user in a text file. - -Compulsory arguments: - list Text file containing a list of squad qc folders - -Optional arguments: - -g, --grouping Text file containing grouping variable for the listed subjects - -u, --update [group_db.json] Update existing eddy_squad reports after generating group report or using a pre-existing [group_db.json] one - -gdb, --group-db Text file containing grouping variable for the database subjects - -o, --output-dir Output directory - default = '.qc' - -Output: - output-dir/group_qc.pdf: study-wise QC report - output-dir/group_db.json: study-wise QC database - -Examples --------- -Assuming qc_folders.txt file is structured as: -subj1/eddy_corrected.qc -subj2/eddy_corrected.qc -subj3/eddy_corrected.qc -... -and group.txt file is structured as (first row is the label): -Group -1 -0 -1 -... - -Minimal running style: - eddy_squad qc_folders.txt - This will generate a quad directory where group_db.json (database) and group_qc.pdf (report) will be stored. -Complete running style: - eddy_squad qc_folders.txt -u -g group.txt -o quad_group - This will generate a quad_group directory where group_db.json (database) and group_qc.pdf (report) will be stored. Individual subjects' QC reports previously generated by QUAD will be updated by adding extra pages that will show the single sunject in the context of the study and marking QC indices as outliers in the tables where needed. Extra pages will be added to the report where distributions for individual QC indices will account for the specified grouping variable. -Using a previously generated database: - eddy_squad qc_folders.txt -u study/group_db.json -g group.txt -gdb group_db.txt -o quad_group - Same as before, but this time we are using a previously generated database to update the single subject reports. !!!NB!!! If using a grouping variable, it is required to specify the same grouping variable for the subjects of the previously generated database as a different variable. From c7d3f6abfb8a00602ae617c37d23ccedfabfa2ab Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:46:34 -0400 Subject: [PATCH 15/18] Delete requirements.txt --- docker/src/eddy-qc/requirements.txt | 5 ----- 1 file changed, 5 deletions(-) delete mode 100644 docker/src/eddy-qc/requirements.txt diff --git a/docker/src/eddy-qc/requirements.txt b/docker/src/eddy-qc/requirements.txt deleted file mode 100644 index f320138..0000000 --- a/docker/src/eddy-qc/requirements.txt +++ /dev/null @@ -1,5 +0,0 @@ -nibabel==2.* -scipy -matplotlib -seaborn -PyPDF2 From c53f2222e866399901e34ae05aabec5ad32abab3 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:46:44 -0400 Subject: [PATCH 16/18] Delete setup.py --- docker/src/eddy-qc/setup.py | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 docker/src/eddy-qc/setup.py diff --git a/docker/src/eddy-qc/setup.py b/docker/src/eddy-qc/setup.py deleted file mode 100644 index 625627c..0000000 --- a/docker/src/eddy-qc/setup.py +++ /dev/null @@ -1,11 +0,0 @@ -from setuptools import setup,find_packages -with open('requirements.txt', 'rt') as f: - install_requires = [l.strip() for l in f.readlines()] - -setup(name='eddy_qc', - version='1.0.0', - description='EDDY Quality Control tools', - author='Matteo Bastiani', - install_requires=install_requires, - scripts=['eddy_qc/scripts/eddy_squad','eddy_qc/scripts/eddy_quad'], - packages=find_packages()) From 231d80cdb48cec781c8ce2946955e232b1f34a2e Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 11:47:54 -0400 Subject: [PATCH 17/18] change from qc_json to out_qc_json --- dmriprep/run.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/dmriprep/run.py b/dmriprep/run.py index 8829775..d1dec6d 100644 --- a/dmriprep/run.py +++ b/dmriprep/run.py @@ -755,13 +755,13 @@ def binarize_aparc(aparc_aseg): wf.connect(scale_tensor_eddy, "out_file", datasink, "dmriprep.dti_eddy.@scaled_tensor") # all the eddy_quad stuff - wf.connect(eddy_quad, 'qc_json', datasink, "dmriprep.qc.@eddyquad_json") - wf.connect(eddy_quad, 'qc_pdf', datasink, "dmriprep.qc.@eddyquad_pdf") - wf.connect(eddy_quad, 'avg_b_png', datasink, "dmriprep.qc.@eddyquad_bpng") - wf.connect(eddy_quad, 'avg_b0_pe_png', datasink, "dmriprep.qc.@eddyquad_b0png") - wf.connect(eddy_quad, 'cnr_png', datasink, "dmriprep.qc.@eddyquad_cnr") - wf.connect(eddy_quad, 'vdm_png', datasink, "dmriprep.qc.@eddyquad_vdm") - wf.connect(eddy_quad, 'residuals', datasink, 'dmriprep.qc.@eddyquad_resid') + wf.connect(eddy_quad, 'out_qc_json', datasink, "dmriprep.qc.@eddyquad_json") + wf.connect(eddy_quad, 'out_qc_pdf', datasink, "dmriprep.qc.@eddyquad_pdf") + wf.connect(eddy_quad, 'out_avg_b_png', datasink, "dmriprep.qc.@eddyquad_bpng") + wf.connect(eddy_quad, 'out_avg_b0_pe_png', datasink, "dmriprep.qc.@eddyquad_b0png") + wf.connect(eddy_quad, 'out_cnr_png', datasink, "dmriprep.qc.@eddyquad_cnr") + wf.connect(eddy_quad, 'out_vdm_png', datasink, "dmriprep.qc.@eddyquad_vdm") + wf.connect(eddy_quad, 'out_residuals', datasink, 'dmriprep.qc.@eddyquad_resid') # anatomical registration stuff wf.connect(bbreg, "min_cost_file", datasink, "dmriprep.reg.@mincost") @@ -793,7 +793,7 @@ def report_fn(dwi_corrected_file, eddy_rms, eddy_report, # for the report, lets show the eddy corrected (full volume) image wf.connect(voltransform, "transformed_file", report_node, 'dwi_corrected_file') - wf.connect(eddy_quad, 'qc_json', report_node, 'eddy_qc_file') + wf.connect(eddy_quad, 'out_qc_json', report_node, 'eddy_qc_file') # add the rms movement output from eddy wf.connect(prep, "fsl_eddy.out_movement_rms", report_node, 'eddy_rms') From 44efdbcfdd8cb8b5ce342495edd2402d58428518 Mon Sep 17 00:00:00 2001 From: nrajamani3 Date: Tue, 12 Mar 2019 12:11:30 -0400 Subject: [PATCH 18/18] possible change in pybids