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Mouse-Imaging-Centre
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pydpiper
Python code for flexible pipeline control
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Feature Request: cleanup command
#417
gdevenyi
opened
5 years ago
0
Cluster interface: special casing for SGE memory?
#416
gdevenyi
opened
5 years ago
2
CSV column for MAGeT mask?
#415
gdevenyi
opened
5 years ago
4
twolevel_model_building imports the input csv twice
#414
nzxwang
opened
5 years ago
0
problems with CSV file merging
#413
bcdarwin
closed
5 years ago
5
Document/publish pydpiper resources
#412
gdevenyi
opened
5 years ago
5
Current ITK tools status
#411
gdevenyi
opened
5 years ago
1
2.0.12 --help registration/execution sections out of order.
#410
gdevenyi
opened
5 years ago
0
Protocols for Neonates and/or recommended settings?
#409
gdevenyi
opened
5 years ago
8
pydpiper 2.0.12 (v2) prints a bunch of warnings under default/recommended configuration
#408
gdevenyi
opened
5 years ago
3
Rerunning complete pipelines give ambiguous status output
#407
gdevenyi
opened
5 years ago
0
Please don't forcepush and/or delete/re-release versions :(
#406
gdevenyi
closed
5 years ago
2
--resolution option should resample rather than autocrop mask
#405
gdevenyi
opened
5 years ago
0
Feature Request: Upgrade check_pipeline_status.py to indicate where things are in the "lsq6 -> lsq12 -> nlin" staging
#404
gdevenyi
opened
5 years ago
0
pydpiper/2.0.12 MAGeT.py with outputdir fails to start, can't find segmentations.csv
#403
gdevenyi
opened
5 years ago
5
twolevel_model_building.py + MAGeT produces a ton of per-scan directories in outputdir
#402
gdevenyi
opened
5 years ago
0
pydpiper/2.0.12 twolevel_model_building.py fails to start with --run-maget
#401
gdevenyi
opened
5 years ago
3
pydpiper/2.0.12 twolevel_model_building.py fails to start with --no-run-maget
#400
gdevenyi
closed
5 years ago
1
pydpiper 2.0.12 NEWS typo PNG->JPG
#399
gdevenyi
closed
5 years ago
0
Newer minc-toolkit versions have a -labels option
#398
gdevenyi
closed
5 years ago
2
Newer antsApplyTransforms has GenericLabel interpolator
#397
gdevenyi
opened
5 years ago
0
Negative values and sinc/bspline interpolation
#396
gdevenyi
opened
5 years ago
0
pydpiper 2.0.12, no-op invocations produce a log file
#395
gdevenyi
opened
5 years ago
0
pydpiper 2.0.12 pipeline_executor.py fails if PYDPIPER_CONFIG_FILE is undefined in environment
#394
gdevenyi
closed
5 years ago
4
Pandas deprecation warning in 2.0.12 regarding select
#393
gdevenyi
closed
5 years ago
0
pydpiper 2.0.12 --help for common space is wrong
#392
gdevenyi
closed
5 years ago
2
move protocols in applications_testing to a more sensible place
#391
bcdarwin
opened
5 years ago
1
pydpiper 2.0.12 won't run with defaults (missing configured default protocols)
#390
gdevenyi
opened
5 years ago
8
--resolution option should specify units
#389
gdevenyi
opened
5 years ago
4
Implement --dump-config option?
#388
gdevenyi
opened
5 years ago
0
Python's builtin typing version 3.6.6 breaks get_model_building_procedure
#387
nzxwang
closed
5 years ago
16
[Documentation Request] Simple pipeline demonstrating how to write pipelines
#386
cfhammill
opened
5 years ago
6
use Vlad's Scipy-based xfmavg
#385
bcdarwin
closed
5 years ago
6
Possibly make better use of (local) temporary directories for cluster submission IO?
#384
gdevenyi
opened
5 years ago
4
ImageMagick QC images are broken for some versions of imagemagick
#383
gdevenyi
closed
5 years ago
1
--csv-file behaves differently for twolevel_model_building.py
#382
nzxwang
closed
5 years ago
1
Apply prefix to all files/directories produced by pydpiper
#381
gdevenyi
opened
5 years ago
0
add flag to relative paths in CSV files
#380
bcdarwin
opened
5 years ago
0
large-rotations setting doesn't do iterative lsq6 registration
#379
bcdarwin
opened
5 years ago
1
very large vmem usage
#378
bcdarwin
closed
4 years ago
2
Better Singularity integration?
#377
bcdarwin
closed
1 year ago
3
get rid of annoying restrictions on input filenames
#376
bcdarwin
opened
5 years ago
0
When additional registration to common space is performed, create overall determinants
#375
bcdarwin
closed
4 years ago
1
strip whitespace from filenames in csvs
#374
bcdarwin
closed
5 years ago
1
--output-dir flag breaks anything that calls create_quality_control_images
#373
nzxwang
closed
4 years ago
2
pydpiper doesn't catch missing config file specified via PYDPIPER_CONFIG_FILE
#372
gdevenyi
closed
5 years ago
0
Use additional information to find LSQ6 transform?
#371
bcdarwin
opened
6 years ago
2
some files (ex. 'pipeline.log') is output to working dir and not --output-dir
#370
nzxwang
closed
4 years ago
2
qbatch now has a python API
#369
gdevenyi
opened
6 years ago
1
If CmdStage.output ==0, CmdStage.log_file will be None
#368
nzxwang
closed
6 years ago
1
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