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fix: to have recon-all work with 5.3 on OSX #1454

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Merged
merged 8 commits into from
Apr 26, 2016
Merged

fix: to have recon-all work with 5.3 on OSX #1454

merged 8 commits into from
Apr 26, 2016

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satra
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@satra satra commented Apr 24, 2016

@dgellis90 and @hjmjohnson - could you please take a look at these changes? this did allow running from start to finish.

from nipype import config
config.enable_provenance()
import os
from nipype.workflows.smri.freesurfer import create_reconall_workflow
recon_all = create_reconall_workflow()
recon_all.inputs.inputspec.subject_id = 'time'
recon_all.inputs.inputspec.subjects_dir = os.getcwd()
recon_all.inputs.inputspec.T1_files = os.path.abspath('mprage003.nii.gz')
recon_all.base_dir = os.getcwd()
recon_all.run(plugin='MultiProc', plugin_args={'n_procs': 4})

also subject_id did not seem to get carried along into the sub commands. so i saw commands like this where the --subject is called with subejct_id instead of 'time' as i used in calling the workflow.

Running: mri_segstats --brainmask brainmask.mgz --ctab /Applications/freesurfer/WMParcStatsLUT.txt
 --etiv --excludeid 0 --in /software/temp/share_blake/ReconAll/AutoRecon2/CA_Normalize/norm.mgz
 --in-intensity-name norm --in-intensity-units MR --pv /software/temp/share_blake/ReconAll/AutoRecon2/CA_Normalize/norm.mgz --seg 
/software/temp/share_blake/ReconAll/AutoRecon3/WM_Parcellation/wmparc.mgz --subject subject_id
 --surf-wm-vol --sum ./wmparc.stats```

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Coverage Status

Coverage remained the same at 72.528% when pulling bf46eef on satra:fix/reconwf into a8e3730 on nipy:master.

@ellisdg
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ellisdg commented Apr 25, 2016

I think the changes look good. I made a PR to your branch that adds an explanation how the subject_id is handled in the workflow.

@satra
Merge pull request #29 from BRAINSia/subjectid
6e40eac 
DOC: Explains how subject_id is used in the workflow
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Coverage Status

Coverage remained the same at 72.528% when pulling 6e40eac on satra:fix/reconwf into a8e3730 on nipy:master.

@satra satra merged commit d6be1d5 into nipy:master Apr 26, 2016
@satra satra deleted the fix/reconwf branch October 30, 2017 15:14
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@satra @coveralls @ellisdg