search

Mouse-Imaging-Centre / pydpiper

Python code for flexible pipeline control
Other
25 stars 10 forks source link

MAGeT.py voxel_vote.py "incorrect number of arguments" #176

Closed gdevenyi closed 9 years ago

gdevenyi commented 9 years ago

Running MAGeT.py like this:

MAGeT.py --queue-type=sge --num-executors=60 --proc=1 --mem=3 \
    --verbose --pipeline-name=D2KO-MAGET \
    --atlas-library ./atlases \
    --output-dir output \
    --lsq12-protocol /opt/quarantine/pydpiper/1.11/src/pydpiper-1.11/applications_testing/test_data/default_linear_MAGeT_prot.csv \
    --nlin-protocol /opt/quarantine/pydpiper/1.11/src/pydpiper-1.11/applications_testing/test_data/default_nlin_MAGeT_minctracc_prot.csv \
    inputs/*.mnc

Pipeline reports the following error

Running on: ciccs03 at 2015-02-05 19:28:42.035372
       voxel_vote /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20150112_BGI_D2K313_4172_FISP-resampled-lsq12/labels/RMS.20150112_BGI_D2K313_4172_FISP-resampled-lsq12_votedlabels.m
       Usage: Usage text
voxel_vote: error: Incorrect number of arguments
jasonlerch commented 9 years ago

I don’t fully understand this error - looks to me like there was only a single file passed into voxel_vote, which needs more than one to vote (for obvious reasons). Any chance that your input consisted of a single file only?

On Feb 6, 2015, at 9:19 AM, Gabriel A. Devenyi notifications@github.com wrote:

Running MAGeT.py like this:

MAGeT.py --queue-type=sge --num-executors=60 --proc=1 --mem=3 \ --verbose --pipeline-name=D2KO-MAGET \ --atlas-library ./atlases \ --output-dir output \ --lsq12-protocol /opt/quarantine/pydpiper/1.11/src/pydpiper-1.11/applications_testing/test_data/default_linear_MAGeT_prot.csv \ --nlin-protocol /opt/quarantine/pydpiper/1.11/src/pydpiper-1.11/applications_testing/test_data/default_nlin_MAGeT_minctracc_prot.csv \ inputs/*.mnc Pipeline reports the following error

Running on: ciccs03 at 2015-02-05 19:28:42.035372 voxel_vote /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20150112_BGI_D2K313_4172_FISP-resampled-lsq12/labels/RMS.20150112_BGI_D2K313_4172_FISP-resampled-lsq12_votedlabels.m Usage: Usage text voxel_vote: error: Incorrect number of arguments — Reply to this email directly or view it on GitHub https://github.com/Mouse-Imaging-Centre/pydpiper/issues/176.

gdevenyi commented 9 years ago

Nope, my input was a nice long list. I think MAGET.py is having issues similar to #172 on my grid engine which triggered this somehow.

gdevenyi commented 9 years ago

Hrm, I think there might be something wrong with the pipeline ordering, here's my pipeline call:

MAGeT.py --queue-type=sge --num-executors=60 --proc=1 --mem=3 \
    --verbose --pipeline-name=D2KO-MAGET \
    --atlas-library ./atlases \
    --output-dir output \
    --lsq12-protocol /opt/quarantine/pydpiper/git/src/pydpiper/applications_testing/test_data/default_linear_MAGeT_prot.csv \
    --nlin-protocol /opt/quarantine/pydpiper/git/src/pydpiper/applications_testing/test_data/default_nlin_MAGeT_minctracc_prot.csv \
    --no-monitor-heartbeats \
    inputs/*.mnc

Here's the logfile:

[2015-02-10 10:05:32.239,Pyro4,INFO] Pyro log configured using built-in defaults, level=INFO
[2015-02-10 10:05:32.728,pydpiper.application,INFO] Calling `start`
[2015-02-10 10:05:32.741,pydpiper.application,INFO] Command is: /opt/quarantine/pydpiper/git/build/bin/MAGeT.py --queue-type=sge --num-executors=60 --proc=1 --mem=3 --verbose --pipeline-name=D2KO-MAGET --atlas-library ./atlases --output-dir output --lsq12-protocol /opt/quarantine/pydpiper/git/src/pydpiper/applications_testing/test_data/default_linear_MAGeT_prot.csv --nlin-protocol /opt/quarantine/pydpiper/git/src/pydpiper/applications_testing/test_data/default_nlin_MAGeT_minctracc_prot.csv --no-monitor-heartbeats inputs/RMS.20141029_BGI_D2K011_3293_FISP-resampled-lsq12.mnc inputs/RMS.20141029_BGI_D2K011_3551_FISP-resampled-lsq12.mnc inputs/RMS.20141029_BGI_D2K011_4578_FISP-resampled-lsq12.mnc inputs/RMS.20141029_BGI_D2K011_4590_FISP-resampled-lsq12.mnc inputs/RMS.20141029_BGI_D2K021_3553_FISP-resampled-lsq12.mnc inputs/RMS.20141029_BGI_D2K021_4160_FISP-resampled-lsq12.mnc inputs/RMS.20141029_BGI_D2K021_4577_FISP-resampled-lsq12.mnc inputs/RMS.20141029_BGI_D2K021_4581_FISP-resampled-lsq12.mnc inputs/RMS.20141103_BGI_D2K011_4161_FISP-resampled-lsq12.mnc inputs/RMS.20141103_BGI_D2K011_4598_FISP-resampled-lsq12.mnc inputs/RMS.20141103_BGI_D2K011_5201_FISP-resampled-lsq12.mnc inputs/RMS.20141103_BGI_D2K011_5203_FISP-resampled-lsq12.mnc inputs/RMS.20141103_BGI_D2K021_4163_FISP-resampled-lsq12.mnc inputs/RMS.20141103_BGI_D2K021_4580_FISP-resampled-lsq12.mnc inputs/RMS.20141103_BGI_D2K021_5196_FISP-resampled-lsq12.mnc inputs/RMS.20141103_BGI_D2K021_5206_FISP-resampled-lsq12.mnc inputs/RMS.20141105_BGI_D2K012_3282_FISP-resampled-lsq12.mnc inputs/RMS.20141105_BGI_D2K012_3295_FISP-resampled-lsq12.mnc inputs/RMS.20141105_BGI_D2K012_4587_FISP-resampled-lsq12.mnc inputs/RMS.20141105_BGI_D2K012_4593_FISP-resampled-lsq12.mnc inputs/RMS.20141105_BGI_D2K021_4573_FISP-resampled-lsq12.mnc inputs/RMS.20141105_BGI_D2K022_3286_FISP-resampled-lsq12.mnc inputs/RMS.20141105_BGI_D2K022_3545_FISP-resampled-lsq12.mnc inputs/RMS.20141105_BGI_D2K022_4579_FISP-resampled-lsq12.mnc inputs/RMS.20141107_BGI_D2K012_4164_FISP-resampled-lsq12.mnc inputs/RMS.20141107_BGI_D2K012_4596_FISP-resampled-lsq12.mnc inputs/RMS.20141107_BGI_D2K012_5174_FISP-resampled-lsq12.mnc inputs/RMS.20141107_BGI_D2K012_5199_FISP-resampled-lsq12.mnc inputs/RMS.20141107_BGI_D2K022_4165_FISP-resampled-lsq12.mnc inputs/RMS.20141107_BGI_D2K022_4591_FISP-resampled-lsq12.mnc inputs/RMS.20141107_BGI_D2K022_4601_FISP-resampled-lsq12.mnc inputs/RMS.20141107_BGI_D2K022_5180_FISP-resampled-lsq12.mnc inputs/RMS.20141111_BGI_D2K013_3544_FISP-resampled-lsq12.mnc inputs/RMS.20141111_BGI_D2K013_3546_FISP-resampled-lsq12.mnc inputs/RMS.20141111_BGI_D2K013_4572_FISP-resampled-lsq12.mnc inputs/RMS.20141111_BGI_D2K013_4586_FISP-resampled-lsq12.mnc inputs/RMS.20141111_BGI_D2K023_3547_FISP-resampled-lsq12.mnc inputs/RMS.20141111_BGI_D2K023_3548_FISP-resampled-lsq12.mnc inputs/RMS.20141111_BGI_D2K023_4575_FISP-resampled-lsq12.mnc inputs/RMS.20141111_BGI_D2K023_4585_FISP-resampled-lsq12.mnc inputs/RMS.20141112_BGI_D2K013_4172_FISP-resampled-lsq12.mnc inputs/RMS.20141112_BGI_D2K013_5182_FISP-resampled-lsq12.mnc inputs/RMS.20141112_BGI_D2K013_5191_FISP-resampled-lsq12.mnc inputs/RMS.20141112_BGI_D2K013_5195_FISP-resampled-lsq12.mnc inputs/RMS.20141112_BGI_D2K023_4171_FISP-resampled-lsq12.mnc inputs/RMS.20141112_BGI_D2K023_4604_FISP-resampled-lsq12.mnc inputs/RMS.20141112_BGI_D2K023_5173_FISP-resampled-lsq12.mnc inputs/RMS.20141112_BGI_D2K023_5202_FISP-resampled-lsq12.mnc inputs/RMS.20141124_BGI_D2K111_3293_FISP-resampled-lsq12.mnc inputs/RMS.20141124_BGI_D2K111_3551_FISP-resampled-lsq12.mnc inputs/RMS.20141124_BGI_D2K111_4578_FISP-resampled-lsq12.mnc inputs/RMS.20141124_BGI_D2K111_4590_FISP-resampled-lsq12.mnc inputs/RMS.20141124_BGI_D2K121_3553_FISP-resampled-lsq12.mnc inputs/RMS.20141124_BGI_D2K121_4160_FISP-resampled-lsq12.mnc inputs/RMS.20141124_BGI_D2K121_4577_FISP-resampled-lsq12.mnc inputs/RMS.20141124_BGI_D2K121_4581_FISP-resampled-lsq12.mnc inputs/RMS.20141125_BGI_D2K111_4161_FISP-resampled-lsq12.mnc inputs/RMS.20141125_BGI_D2K111_4598_FISP-resampled-lsq12.mnc inputs/RMS.20141125_BGI_D2K111_5201_FISP-resampled-lsq12.mnc inputs/RMS.20141125_BGI_D2K111_5203_FISP-resampled-lsq12.mnc inputs/RMS.20141125_BGI_D2K121_4163_FISP-resampled-lsq12.mnc inputs/RMS.20141125_BGI_D2K121_4580_FISP-resampled-lsq12.mnc inputs/RMS.20141125_BGI_D2K121_5196_FISP-resampled-lsq12.mnc inputs/RMS.20141125_BGI_D2K121_5206_FISP-resampled-lsq12.mnc inputs/RMS.20141126_BGI_D2K112_3282_FISP-resampled-lsq12.mnc inputs/RMS.20141126_BGI_D2K112_3295_FISP-resampled-lsq12.mnc inputs/RMS.20141126_BGI_D2K112_4587_FISP-resampled-lsq12.mnc inputs/RMS.20141126_BGI_D2K112_4593_FISP-resampled-lsq12.mnc inputs/RMS.20141126_BGI_D2K122_3286_FISP-resampled-lsq12.mnc inputs/RMS.20141126_BGI_D2K122_3545_FISP-resampled-lsq12.mnc inputs/RMS.20141126_BGI_D2K122_4573_FISP-resampled-lsq12.mnc inputs/RMS.20141126_BGI_D2K122_4579_FISP-resampled-lsq12.mnc inputs/RMS.20141128_BGI_D2K112_4164_FISP-resampled-lsq12.mnc inputs/RMS.20141128_BGI_D2K112_4596_FISP-resampled-lsq12.mnc inputs/RMS.20141128_BGI_D2K112_5174_FISP-resampled-lsq12.mnc inputs/RMS.20141128_BGI_D2K112_5199_FISP-resampled-lsq12.mnc inputs/RMS.20141128_BGI_D2K122_4165_FISP-resampled-lsq12.mnc inputs/RMS.20141128_BGI_D2K122_4591_FISP-resampled-lsq12.mnc inputs/RMS.20141128_BGI_D2K122_4601_FISP-resampled-lsq12.mnc inputs/RMS.20141128_BGI_D2K122_5180_FISP-resampled-lsq12.mnc inputs/RMS.20141201_BGI_D2K113_3544_FISP-resampled-lsq12.mnc inputs/RMS.20141201_BGI_D2K113_3546_FISP-resampled-lsq12.mnc inputs/RMS.20141201_BGI_D2K113_4572_FISP-resampled-lsq12.mnc inputs/RMS.20141201_BGI_D2K113_4586_FISP-resampled-lsq12.mnc inputs/RMS.20141201_BGI_D2K123_3547_FISP-resampled-lsq12.mnc inputs/RMS.20141201_BGI_D2K123_3548_FISP-resampled-lsq12.mnc inputs/RMS.20141201_BGI_D2K123_4575_FISP-resampled-lsq12.mnc inputs/RMS.20141201_BGI_D2K123_4585_FISP-resampled-lsq12.mnc inputs/RMS.20141202_BGI_D2K113_4172_FISP-resampled-lsq12.mnc inputs/RMS.20141202_BGI_D2K113_5182_FISP-resampled-lsq12.mnc inputs/RMS.20141202_BGI_D2K113_5191_FISP-resampled-lsq12.mnc inputs/RMS.20141202_BGI_D2K113_5195_FISP-resampled-lsq12.mnc inputs/RMS.20141202_BGI_D2K123_4171_FISP-resampled-lsq12.mnc inputs/RMS.20141202_BGI_D2K123_4604_FISP-resampled-lsq12.mnc inputs/RMS.20141202_BGI_D2K123_5173_FISP-resampled-lsq12.mnc inputs/RMS.20141202_BGI_D2K123_5202_FISP-resampled-lsq12.mnc inputs/RMS.20141215_BGI_D2K211_3293_FISP-resampled-lsq12.mnc inputs/RMS.20141215_BGI_D2K211_3551_FISP-resampled-lsq12.mnc inputs/RMS.20141215_BGI_D2K211_4578_FISP-resampled-lsq12.mnc inputs/RMS.20141215_BGI_D2K211_4590_FISP-resampled-lsq12.mnc inputs/RMS.20141215_BGI_D2K221_3553_FISP-resampled-lsq12.mnc inputs/RMS.20141215_BGI_D2K221_4160_FISP-resampled-lsq12.mnc inputs/RMS.20141215_BGI_D2K221_4577_FISP-resampled-lsq12.mnc inputs/RMS.20141215_BGI_D2K221_4581_FISP-resampled-lsq12.mnc inputs/RMS.20141216_BGI_D2K211_4161_FISP-resampled-lsq12.mnc inputs/RMS.20141216_BGI_D2K211_4598_FISP-resampled-lsq12.mnc inputs/RMS.20141216_BGI_D2K211_5201_FISP-resampled-lsq12.mnc inputs/RMS.20141216_BGI_D2K211_5203_FISP-resampled-lsq12.mnc inputs/RMS.20141216_BGI_D2K221_4163_FISP-resampled-lsq12.mnc inputs/RMS.20141216_BGI_D2K221_4580_FISP-resampled-lsq12.mnc inputs/RMS.20141216_BGI_D2K221_5196_FISP-resampled-lsq12.mnc inputs/RMS.20141216_BGI_D2K221_5206_FISP-resampled-lsq12.mnc inputs/RMS.20141217_BGI_D2K212_3282_FISP-resampled-lsq12.mnc inputs/RMS.20141217_BGI_D2K212_3295_FISP-resampled-lsq12.mnc inputs/RMS.20141217_BGI_D2K212_4587_FISP-resampled-lsq12.mnc inputs/RMS.20141217_BGI_D2K212_4593_FISP-resampled-lsq12.mnc inputs/RMS.20141217_BGI_D2K222_3545_FISP-resampled-lsq12.mnc inputs/RMS.20141217_BGI_D2K222_4573_FISP-resampled-lsq12.mnc inputs/RMS.20141217_BGI_D2K222_4579_FISP-resampled-lsq12.mnc inputs/RMS.20141218_BGI_D2K212_4164_FISP-resampled-lsq12.mnc inputs/RMS.20141218_BGI_D2K212_4596_FISP-resampled-lsq12.mnc inputs/RMS.20141218_BGI_D2K212_5174_FISP-resampled-lsq12.mnc inputs/RMS.20141218_BGI_D2K212_5199_FISP-resampled-lsq12.mnc inputs/RMS.20141218_BGI_D2K222_4165_FISP-resampled-lsq12.mnc inputs/RMS.20141218_BGI_D2K222_4591_FISP-resampled-lsq12.mnc inputs/RMS.20141218_BGI_D2K222_4601_FISP-resampled-lsq12.mnc inputs/RMS.20141218_BGI_D2K222_5180_FISP-resampled-lsq12.mnc inputs/RMS.20141219_BGI_D2K213_3544_FISP-resampled-lsq12.mnc inputs/RMS.20141219_BGI_D2K213_3546_FISP-resampled-lsq12.mnc inputs/RMS.20141219_BGI_D2K213_4572_FISP-resampled-lsq12.mnc inputs/RMS.20141219_BGI_D2K213_4586_FISP-resampled-lsq12.mnc inputs/RMS.20141219_BGI_D2K223_3547_FISP-resampled-lsq12.mnc inputs/RMS.20141219_BGI_D2K223_3548_FISP-resampled-lsq12.mnc inputs/RMS.20141219_BGI_D2K223_4575_FISP-resampled-lsq12.mnc inputs/RMS.20141219_BGI_D2K223_4585_FISP-resampled-lsq12.mnc inputs/RMS.20141222_BGI_D2K213_4172_FISP-resampled-lsq12.mnc inputs/RMS.20141222_BGI_D2K213_5182_FISP-resampled-lsq12.mnc inputs/RMS.20141222_BGI_D2K213_5191_FISP-resampled-lsq12.mnc inputs/RMS.20141222_BGI_D2K213_5195_FISP-resampled-lsq12.mnc inputs/RMS.20141222_BGI_D2K223_4171_FISP-resampled-lsq12.mnc inputs/RMS.20141222_BGI_D2K223_4604_FISP-resampled-lsq12.mnc inputs/RMS.20141222_BGI_D2K223_5173_FISP-resampled-lsq12.mnc inputs/RMS.20141222_BGI_D2K223_5202_FISP-resampled-lsq12.mnc inputs/RMS.20150105_BGI_D2K311_3293_FISP-resampled-lsq12.mnc inputs/RMS.20150105_BGI_D2K311_3551_FISP-resampled-lsq12.mnc inputs/RMS.20150105_BGI_D2K311_4578_FISP-resampled-lsq12.mnc inputs/RMS.20150105_BGI_D2K311_4590_FISP-resampled-lsq12.mnc inputs/RMS.20150105_BGI_D2K321_3553_FISP-resampled-lsq12.mnc inputs/RMS.20150105_BGI_D2K321_4160_FISP-resampled-lsq12.mnc inputs/RMS.20150105_BGI_D2K321_4577_FISP-resampled-lsq12.mnc inputs/RMS.20150105_BGI_D2K321_4581_FISP-resampled-lsq12.mnc inputs/RMS.20150106_BGI_D2K311_4161_FISP-resampled-lsq12.mnc inputs/RMS.20150106_BGI_D2K311_4598_FISP-resampled-lsq12.mnc inputs/RMS.20150106_BGI_D2K311_5201_FISP-resampled-lsq12.mnc inputs/RMS.20150106_BGI_D2K311_5203_FISP-resampled-lsq12.mnc inputs/RMS.20150106_BGI_D2K321_4163_FISP-resampled-lsq12.mnc inputs/RMS.20150106_BGI_D2K321_4580_FISP-resampled-lsq12.mnc inputs/RMS.20150106_BGI_D2K321_5196_FISP-resampled-lsq12.mnc inputs/RMS.20150106_BGI_D2K321_5206_FISP-resampled-lsq12.mnc inputs/RMS.20150107_BGI_D2K312_3282_FISP-resampled-lsq12.mnc inputs/RMS.20150107_BGI_D2K312_3295_FISP-resampled-lsq12.mnc inputs/RMS.20150107_BGI_D2K312_4587_FISP-resampled-lsq12.mnc inputs/RMS.20150107_BGI_D2K312_4593_FISP-resampled-lsq12.mnc inputs/RMS.20150107_BGI_D2K322_3545_FISP-resampled-lsq12.mnc inputs/RMS.20150107_BGI_D2K322_4573_FISP-resampled-lsq12.mnc inputs/RMS.20150107_BGI_D2K322_4579_FISP-resampled-lsq12.mnc inputs/RMS.20150108_BGI_D2K312_4164_FISP-resampled-lsq12.mnc inputs/RMS.20150108_BGI_D2K312_4596_FISP-resampled-lsq12.mnc inputs/RMS.20150108_BGI_D2K312_5174_FISP-resampled-lsq12.mnc inputs/RMS.20150108_BGI_D2K312_5199_FISP-resampled-lsq12.mnc inputs/RMS.20150108_BGI_D2K322_4165_FISP-resampled-lsq12.mnc inputs/RMS.20150108_BGI_D2K322_4591_FISP-resampled-lsq12.mnc inputs/RMS.20150108_BGI_D2K322_4601_FISP-resampled-lsq12.mnc inputs/RMS.20150108_BGI_D2K322_5180_FISP-resampled-lsq12.mnc inputs/RMS.20150109_BGI_D2K313_3544_FISP-resampled-lsq12.mnc inputs/RMS.20150109_BGI_D2K313_3546_FISP-resampled-lsq12.mnc inputs/RMS.20150109_BGI_D2K313_4572_FISP-resampled-lsq12.mnc inputs/RMS.20150109_BGI_D2K313_4586_FISP-resampled-lsq12.mnc inputs/RMS.20150109_BGI_D2K323_3547_FISP-resampled-lsq12.mnc inputs/RMS.20150109_BGI_D2K323_3548_FISP-resampled-lsq12.mnc inputs/RMS.20150109_BGI_D2K323_4575_FISP-resampled-lsq12.mnc inputs/RMS.20150109_BGI_D2K323_4585_FISP-resampled-lsq12.mnc inputs/RMS.20150112_BGI_D2K313_4172_FISP-resampled-lsq12.mnc inputs/RMS.20150112_BGI_D2K313_5182_FISP-resampled-lsq12.mnc inputs/RMS.20150112_BGI_D2K313_5191_FISP-resampled-lsq12.mnc inputs/RMS.20150112_BGI_D2K313_5195_FISP-resampled-lsq12.mnc inputs/RMS.20150112_BGI_D2K323_4171_FISP-resampled-lsq12.mnc inputs/RMS.20150112_BGI_D2K323_4604_FISP-resampled-lsq12.mnc inputs/RMS.20150112_BGI_D2K323_5173_FISP-resampled-lsq12.mnc inputs/RMS.20150112_BGI_D2K323_5202_FISP-resampled-lsq12.mnc
[2015-02-10 10:05:32.741,pydpiper.application,INFO] Command version : 1.11
[2015-02-10 10:05:34.883,atoms_and_modules.registration_functions,INFO] No mask directory specified as command line option. No masks included during RegistrationPipeFH initialization.
[2015-02-10 10:05:43.960,__main__,INFO] Number of input atlas/label pairs: 0
[2015-02-10 10:05:43.960,__main__,INFO] Number of templates created (all input files...): 190
[2015-02-10 10:05:43.960,__main__,INFO] Number of templates used for each inputfile: 0
[2015-02-10 10:05:44.262,pydpiper.pipeline,INFO] Create Edges time: 0.298892021179
[2015-02-10 10:05:44.423,pydpiper.pipeline,INFO] Graph heads: [0, 1, 10, 19, 28, 37, 46, 55, 64, 73, 82, 91, 100, 109, 118, 127, 136, 145, 154, 163, 172, 181, 190, 199, 208, 217, 226, 427, 628, 829, 1030, 1231, 1432, 1633, 1834, 2035, 2236, 2437, 2638, 2839, 3040, 3241, 3442, 3643, 3844, 4045, 4246, 4447, 4648, 4849, 5050, 5251, 5252, 5453, 5454, 5655, 5656, 5857, 5858, 6059, 6060, 6261, 6262, 6463, 6464, 6665, 6666, 6867, 6868, 7069, 7070, 7271, 7272, 7473, 7474, 7675, 7676, 7877, 7878, 8079, 8080, 8281, 8282, 8483, 8484, 8685, 8686, 8887, 8888, 9089, 9090, 9291, 9292, 9493, 9494, 9695, 9696, 9897, 9898, 10099, 10100, 10301, 10302, 10503, 10504, 10705, 10706, 10907, 10908, 11109, 11110, 11311, 11312, 11513, 11514, 11715, 11716, 11917, 11918, 12119, 12120, 12321, 12322, 12523, 12524, 12725, 12726, 12927, 12928, 13129, 13130, 13331, 13332, 13533, 13534, 13735, 13736, 13937, 13938, 14139, 14140, 14341, 14342, 14543, 14544, 14745, 14746, 14947, 14948, 15149, 15150, 15351, 15352, 15553, 15554, 15755, 15756, 15957, 15958, 16159, 16160, 16361, 16362, 16563, 16564, 16765, 16766, 16967, 16968, 17169, 17170, 17371, 17372, 17573, 17574, 17775, 17776, 17977, 17978, 18179, 18180, 18381, 18382, 18583, 18584, 18785, 18786, 18987, 18988, 19189, 19190, 19391, 19392, 19593, 19594, 19795, 19796, 19997, 19998, 20199, 20200, 20401, 20402, 20603, 20604, 20805, 20806, 21007, 21008, 21209, 21210, 21411, 21412, 21613, 21614, 21815, 21816, 22017, 22018, 22219, 22220, 22421, 22422, 22623, 22624, 22825, 22826, 23027, 23028, 23229, 23230, 23431, 23432, 23633, 23634, 23835, 23836, 24037, 24038, 24239, 24240, 24441, 24442, 24643, 24644, 24845, 24846, 25047, 25048, 25249, 25250, 25451, 25452, 25653, 25654, 25855, 25856, 26057, 26058, 26259, 26260, 26461, 26462, 26663, 26664, 26865, 26866, 27067, 27068, 27269, 27270, 27471, 27472, 27673, 27674, 27875, 27876, 28077, 28078, 28279, 28280, 28481, 28482, 28683, 28684, 28885, 28886, 29087, 29088, 29289, 29290, 29491, 29492, 29693, 29694, 29895, 29896, 30097, 30098, 30299, 30300, 30501, 30502, 30703, 30704, 30905, 30906, 31107, 31108, 31309, 31310, 31511, 31512, 31713, 31714, 31915, 31916, 32117, 32118, 32319, 32320, 32521, 32522, 32723, 32724, 32925, 32926, 33127, 33128, 33329, 33330, 33531, 33532, 33733, 33734, 33935, 33936, 34137, 34138, 34339, 34340, 34541, 34542, 34743, 34744, 34945, 34946, 35147, 35148, 35349, 35350, 35551, 35552, 35753, 35754, 35955, 35956, 36157, 36158, 36359, 36360, 36561, 36562, 36763, 36764, 36965, 36966, 37167, 37168, 37369, 37370, 37571, 37572, 37773, 37774, 37975, 37976, 38177, 38178, 38379]
[2015-02-10 10:05:48.511,pydpiper.application,INFO] Starting pipeline daemon...
[2015-02-10 10:05:48.511,pydpiper.pipeline,INFO] Finished stages log doesn't exist or is corrupt.
[2015-02-10 10:05:48.513,Pyro4.multiplexserver,INFO] starting multiplexed socketserver
[2015-02-10 10:05:48.520,pydpiper.pipeline,INFO] Daemon is running at: 172.16.133.224:51201
[2015-02-10 10:05:48.520,pydpiper.pipeline,INFO] The pipeline's uri is: PYRO:obj_cb921f1860c34562afc09d08b8b23342@172.16.133.224:51201
[2015-02-10 10:05:48.525,Pyro4.core,INFO] daemon 172.16.133.224:51201 entering requestloop
[2015-02-10 10:05:48.527,pydpiper.pipeline,INFO] I couldn't determine your remaining walltime from qstat.
[2015-02-10 10:05:48.532,pydpiper.pipeline,INFO] Launching 60 executors
[2015-02-10 10:05:52.606,pydpiper.pipeline,INFO] Starting Stage 0: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141029_BGI_D2K011_3551_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K011_3551_FISP-resampled-lsq12/tmp/RMS.20141029_BGI_D2K011_3551_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_3857af07ec1d471f9fbab36572012fbd@172.16.67.223:35383)
[2015-02-10 10:05:52.647,pydpiper.pipeline,INFO] Starting Stage 1: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141029_BGI_D2K011_3293_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K011_3293_FISP-resampled-lsq12/tmp/RMS.20141029_BGI_D2K011_3293_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_1f2b2f5c0d6041898d9ad618bee7e343@172.16.67.223:41547)
[2015-02-10 10:05:52.648,pydpiper.pipeline,INFO] Starting Stage 10: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141029_BGI_D2K011_4578_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K011_4578_FISP-resampled-lsq12/tmp/RMS.20141029_BGI_D2K011_4578_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_e35a3ea5ad004802a05c925201e56c47@172.16.67.223:49024)
[2015-02-10 10:05:52.758,pydpiper.pipeline,INFO] Starting Stage 19: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141029_BGI_D2K011_4590_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K011_4590_FISP-resampled-lsq12/tmp/RMS.20141029_BGI_D2K011_4590_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_0e283466283148f4aaaea9fb3ca4bad4@172.16.67.223:51523)
[2015-02-10 10:05:52.776,pydpiper.pipeline,INFO] Starting Stage 28: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141029_BGI_D2K021_3553_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K021_3553_FISP-resampled-lsq12/tmp/RMS.20141029_BGI_D2K021_3553_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_4b132375318b45c7b0e7cdf0d9ed5254@172.16.67.223:45977)
[2015-02-10 10:05:52.914,pydpiper.pipeline,INFO] Starting Stage 37: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141029_BGI_D2K021_4160_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K021_4160_FISP-resampled-lsq12/tmp/RMS.20141029_BGI_D2K021_4160_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_517c424eba6149d0b9f6759ac5bbdbc2@172.16.67.227:47756)
[2015-02-10 10:05:52.914,pydpiper.pipeline,INFO] Starting Stage 46: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141029_BGI_D2K021_4577_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K021_4577_FISP-resampled-lsq12/tmp/RMS.20141029_BGI_D2K021_4577_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_fbb4e819f2eb450aafecc81b7b02aec2@172.16.67.227:45411)
[2015-02-10 10:05:52.934,pydpiper.pipeline,INFO] Starting Stage 55: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141029_BGI_D2K021_4581_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K021_4581_FISP-resampled-lsq12/tmp/RMS.20141029_BGI_D2K021_4581_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_6540f35b663349b5ad2b7e6cda37edfb@172.16.67.227:34818)
[2015-02-10 10:05:52.990,pydpiper.pipeline,INFO] Starting Stage 64: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141103_BGI_D2K011_4161_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141103_BGI_D2K011_4161_FISP-resampled-lsq12/tmp/RMS.20141103_BGI_D2K011_4161_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_79def5163af24a8c861d8f81d7ffb505@172.16.67.227:59690)
[2015-02-10 10:05:52.991,pydpiper.pipeline,INFO] Starting Stage 73: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141103_BGI_D2K011_4598_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141103_BGI_D2K011_4598_FISP-resampled-lsq12/tmp/RMS.20141103_BGI_D2K011_4598_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_497542043535453992dd86228451f7fc@172.16.67.227:42702)
[2015-02-10 10:05:53.384,pydpiper.pipeline,INFO] Starting Stage 82: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141103_BGI_D2K011_5201_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141103_BGI_D2K011_5201_FISP-resampled-lsq12/tmp/RMS.20141103_BGI_D2K011_5201_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_f7731cdd05244fd9a93bf00cadc7ee0b@172.16.67.222:46072)
[2015-02-10 10:05:53.385,pydpiper.pipeline,INFO] Starting Stage 91: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141103_BGI_D2K011_5203_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141103_BGI_D2K011_5203_FISP-resampled-lsq12/tmp/RMS.20141103_BGI_D2K011_5203_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_8d1e8e28a4734410a83b312d23cea967@172.16.67.222:34664)
[2015-02-10 10:05:53.389,pydpiper.pipeline,INFO] Starting Stage 100: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141103_BGI_D2K021_4163_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141103_BGI_D2K021_4163_FISP-resampled-lsq12/tmp/RMS.20141103_BGI_D2K021_4163_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_dd287dfe47bc437ea7f9433607c801b7@172.16.67.222:53716)
[2015-02-10 10:05:53.630,pydpiper.pipeline,INFO] Starting Stage 109: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141103_BGI_D2K021_4580_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141103_BGI_D2K021_4580_FISP-resampled-lsq12/tmp/RMS.20141103_BGI_D2K021_4580_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_4293c3c0833f474197a2fc4afe9bcd19@172.16.67.229:35976)
[2015-02-10 10:05:53.631,pydpiper.pipeline,INFO] Starting Stage 118: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141103_BGI_D2K021_5196_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141103_BGI_D2K021_5196_FISP-resampled-lsq12/tmp/RMS.20141103_BGI_D2K021_5196_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_bf682807550b4216a78cf7123755fead@172.16.67.229:59990)
[2015-02-10 10:05:53.638,pydpiper.pipeline,INFO] Starting Stage 127: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141103_BGI_D2K021_5206_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141103_BGI_D2K021_5206_FISP-resampled-lsq12/tmp/RMS.20141103_BGI_D2K021_5206_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_aeabe2c254ef49dca3e14eb537913a38@172.16.67.222:43593)
[2015-02-10 10:05:53.657,pydpiper.pipeline,INFO] Starting Stage 136: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141105_BGI_D2K012_3282_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141105_BGI_D2K012_3282_FISP-resampled-lsq12/tmp/RMS.20141105_BGI_D2K012_3282_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_a99ee6535b1d430a8a2f4deb4ecf1ee2@172.16.67.224:48654)
[2015-02-10 10:05:53.658,pydpiper.pipeline,INFO] Starting Stage 145: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141105_BGI_D2K012_3295_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141105_BGI_D2K012_3295_FISP-resampled-lsq12/tmp/RMS.20141105_BGI_D2K012_3295_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_4fbef0175ac946499ac810268a66f183@172.16.67.222:43522)
[2015-02-10 10:05:53.739,pydpiper.pipeline,INFO] Starting Stage 172: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141105_BGI_D2K021_4573_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141105_BGI_D2K021_4573_FISP-resampled-lsq12/tmp/RMS.20141105_BGI_D2K021_4573_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_70e37ae08998474581c78d755af4b5aa@172.16.67.222:47688)
[2015-02-10 10:05:53.741,pydpiper.pipeline,INFO] Starting Stage 163: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141105_BGI_D2K012_4593_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141105_BGI_D2K012_4593_FISP-resampled-lsq12/tmp/RMS.20141105_BGI_D2K012_4593_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_d4f71b76e78c4604be4325582365947a@172.16.67.222:52843)
[2015-02-10 10:05:53.742,pydpiper.pipeline,INFO] Starting Stage 154: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141105_BGI_D2K012_4587_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141105_BGI_D2K012_4587_FISP-resampled-lsq12/tmp/RMS.20141105_BGI_D2K012_4587_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_45519ec0c8b24bb9a83f24ce29bddf81@172.16.67.229:54873)
[2015-02-10 10:05:53.797,pydpiper.pipeline,INFO] Starting Stage 181: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141105_BGI_D2K022_3286_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141105_BGI_D2K022_3286_FISP-resampled-lsq12/tmp/RMS.20141105_BGI_D2K022_3286_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_942b36ef1eb44b8c8b00785586a60566@172.16.67.229:39289)
[2015-02-10 10:05:53.809,pydpiper.pipeline,INFO] Starting Stage 190: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141105_BGI_D2K022_3545_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141105_BGI_D2K022_3545_FISP-resampled-lsq12/tmp/RMS.20141105_BGI_D2K022_3545_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_d6c476464d394a15b7b16dce58688b4c@172.16.67.224:42441)
[2015-02-10 10:05:53.819,pydpiper.pipeline,INFO] Starting Stage 208: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141107_BGI_D2K012_4164_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141107_BGI_D2K012_4164_FISP-resampled-lsq12/tmp/RMS.20141107_BGI_D2K012_4164_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_79f908d8885b4994bd1c9fc16a16f906@172.16.67.224:46739)
[2015-02-10 10:05:53.933,pydpiper.pipeline,INFO] Starting Stage 199: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141105_BGI_D2K022_4579_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141105_BGI_D2K022_4579_FISP-resampled-lsq12/tmp/RMS.20141105_BGI_D2K022_4579_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_c9b5ba095c8e481db39cdfcb8b68014b@172.16.67.229:37588)
[2015-02-10 10:05:53.949,pydpiper.pipeline,INFO] Starting Stage 217: mincblur -clobber -no_apodize -fwhm 0.25 /data/chamal/projects/gabriel/gumeli-MAGET/inputs/RMS.20141107_BGI_D2K012_4596_FISP-resampled-lsq12.mnc /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141107_BGI_D2K012_4596_FISP-resampled-lsq12/tmp/RMS.20141107_BGI_D2K012_4596_FISP-resampled-lsq12_fwhm0.25 -gradient(PYRO:obj_2593838e618b4c97a09b6eca1c5e214f@172.16.67.229:53700)
[2015-02-10 10:05:53.978,pydpiper.pipeline,INFO] Starting Stage 427: voxel_vote /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K011_3551_FISP-resampled-lsq12/labels/RMS.20141029_BGI_D2K011_3551_FISP-resampled-lsq12_votedlabels.mnc(PYRO:obj_a205468546dc42b885b7fea63f817086@172.16.67.220:51664)
[2015-02-10 10:05:54.036,pydpiper.pipeline,INFO] Starting Stage 628: voxel_vote /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K011_4578_FISP-resampled-lsq12/labels/RMS.20141029_BGI_D2K011_4578_FISP-resampled-lsq12_votedlabels.mnc(PYRO:obj_371480bea4934a35807eced7f45933e9@172.16.67.224:58813)
[2015-02-10 10:05:54.040,pydpiper.pipeline,INFO] Starting Stage 226: voxel_vote /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K011_3293_FISP-resampled-lsq12/labels/RMS.20141029_BGI_D2K011_3293_FISP-resampled-lsq12_votedlabels.mnc(PYRO:obj_72d83ed09c7b4bcda20dc22080b43cbf@172.16.67.229:40074)
[2015-02-10 10:05:54.041,pydpiper.pipeline,INFO] Starting Stage 829: voxel_vote /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K011_4590_FISP-resampled-lsq12/labels/RMS.20141029_BGI_D2K011_4590_FISP-resampled-lsq12_votedlabels.mnc(PYRO:obj_2613b1e6ae7f4fafb776733e20e0c704@172.16.67.220:50897)
[2015-02-10 10:05:54.055,pydpiper.pipeline,INFO] Starting Stage 1030: voxel_vote /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K021_3553_FISP-resampled-lsq12/labels/RMS.20141029_BGI_D2K021_3553_FISP-resampled-lsq12_votedlabels.mnc(PYRO:obj_b506a6bc4db74d25aff4b971c56cdf97@172.16.67.221:51743)
[2015-02-10 10:05:54.063,pydpiper.pipeline,INFO] Starting Stage 1231: voxel_vote /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K021_4160_FISP-resampled-lsq12/labels/RMS.20141029_BGI_D2K021_4160_FISP-resampled-lsq12_votedlabels.mnc(PYRO:obj_91fc7cf9f1924a2e9122a4dde7a52b1a@172.16.67.220:34940)
[2015-02-10 10:05:54.064,pydpiper.pipeline,INFO] Starting Stage 1432: voxel_vote /data/chamal/projects/gabriel/gumeli-MAGET/output/RMS.20141029_BGI_D2K021_4577_FISP-resampled-lsq12/labels/RMS.20141029_BGI_D2K021_4577_FISP-resampled-lsq12_votedlabels.mnc(PYRO:obj_bbfd19b3439b4408aa11783a8aec58ae@172.16.67.224:44769)

I'm surprised to see voxel_vote running before any registration has been done...

gdevenyi commented 9 years ago

This is run against develop 2c0da07ac36646043b100fe1911963673a4c9986

bcdarwin commented 9 years ago

What's in your atlas directory? It could be that Pydpiper doesn't like what's there but doesn't give an informative error message.

mcvaneede commented 9 years ago

The issue is related to your atlas library. The 6th line in the log file you provided states:

[2015-02-10 10:05:43.960,main,INFO] Number of input atlas/label pairs: 0

That means that MAGeT.py did not find any "useful" atlases. I will update the code such that it will exit with an error message when it does not find any atlases. The current assumption is that for each atlas you'll need:

{atlas}_average.mnc {atlas}_labels.mnc {atlas}_mask.mnc

or (different naming convention also possible):

{atlas}.mnc {atlas}_labels.mnc {atlas}_mask.mnc

gdevenyi commented 9 years ago

Well that explains the problem my files were named wrong. On Feb 11, 2015 4:00 PM, "Matthijs van Eede" notifications@github.com wrote:

The issue is related to your atlas library. The 6th line in log file you provided states:

[2015-02-10 10:05:43.960,main,INFO] Number of input atlas/label pairs: 0

That means that MAGeT.py did not find any "useful" atlases. I will update the code such that it will exit with an error message when it does not find any atlases. The current assumption is that for each atlas you'll need:

{atlas}_average.mnc {atlas}_labels.mnc {atlas}_mask.mnc

— Reply to this email directly or view it on GitHub https://github.com/Mouse-Imaging-Centre/pydpiper/issues/176#issuecomment-73963629 .

gdevenyi commented 9 years ago

I was trying to run it against this atlas http://www.mouseimaging.ca/technologies/mouse_atlas/C57Bl6j_mouse_atlas.html

but sadly it has no mask file.

mcvaneede commented 9 years ago

It's quite easy to generate a mask from the labels file. For that 30 micron file, this should produce a good mask:

mincmorph -clobber -successive 'B[0.5:999]DDDDDDDDDDDDEEEEEE' c57_fixed_labels_resized.mnc mask.mnc

gdevenyi commented 9 years ago

Thanks, mask generation sorted.

Your commit also saved me some headaches when I mis-spelled the atlases directory!