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BUG: Freesurfer modules re-written.
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The freesurfer scripts were not internally consistent, nor were they
correct.  A line-by-line review was done diagramming what the inputs/outputs
were for each stage, regularizing the variable names and meanings across the
different stages of running, and verifying that the correct paths were being
created.
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@hjmjohnson
hjmjohnson committed Feb 5, 2013
1 parent 9739816 commit e9c2f06
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Showing 4 changed files with 135 additions and 146 deletions.
106 changes: 48 additions & 58 deletions AutoWorkup/WorkupT1T2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -700,8 +700,8 @@ def WorkupT1T2(subjectid, mountPrefix, ExperimentBaseDirectoryCache, ExperimentB
myLocalSegWF = dict()
SEGMENTATION_DataSink = dict()
STAPLE_SEGMENTATION_DataSink = dict()
myLocalFSWF = dict()
FSPREP_DataSink = dict()
FSCROSS_WF = dict()
FSPREP_DS = dict()
FSCROSS_DS = dict()

MergeStage2AverageImages = dict()
Expand All @@ -713,7 +713,7 @@ def WorkupT1T2(subjectid, mountPrefix, ExperimentBaseDirectoryCache, ExperimentB
LinearSubjectToAtlasANTsApplyTransforms = dict()
MultiLabelSubjectToAtlasANTsApplyTransforms = dict()
Subj2Atlas_DS = dict()
FSBASE_DataSink = dict()
FSBASE_DS = dict()

if 'SEGMENTATION' in WORKFLOW_COMPONENTS: # Run the ANTS Registration from Atlas to Subject for BCut spatial priors propagation.
import PipeLineFunctionHelpers
Expand Down Expand Up @@ -1055,90 +1055,81 @@ def WorkupT1T2(subjectid, mountPrefix, ExperimentBaseDirectoryCache, ExperimentB
if RunMultiMode:
# If multi-modal, then create synthesized image before running
print("HACK FREESURFER len(global_All3T_T2s) > 0 ")
myLocalFSWF[sessionid] = CreateFreeSurferWorkflow_custom(projectid, subjectid, sessionid,
FSCROSS_WF[sessionid] = CreateFreeSurferWorkflow_custom(projectid, subjectid, sessionid,
"FSCROSS", CLUSTER_QUEUE,
CLUSTER_QUEUE_LONG,
RunAllFSComponents,
RunMultiMode,
constructed_FS_SUBJECTS_DIR)
FREESURFER_ID[sessionid] = pe.Node(interface=IdentityInterface(fields=['FreeSurfer_ID']),
FREESURFER_ID[sessionid] = pe.Node(interface=IdentityInterface(fields=['subj_session_id']),
run_without_submitting=True,
name='99_FSNodeName' + str(subjectid) + "_" + str(sessionid))
FREESURFER_ID[sessionid].inputs.FreeSurfer_ID = str(subjectid) + "_" + str(sessionid)
FREESURFER_ID[sessionid].inputs.subj_session_id = str(subjectid) + "_" + str(sessionid)

baw200.connect(PHASE_2_oneSubjWorkflow[sessionid], 'outputspec.t1_average', myLocalFSWF[sessionid], 'inputspec.T1_files')
baw200.connect(PHASE_2_oneSubjWorkflow[sessionid], 'outputspec.t2_average', myLocalFSWF[sessionid], 'inputspec.T2_files')
baw200.connect(PHASE_2_oneSubjWorkflow[sessionid], 'outputspec.outputLabels', myLocalFSWF[sessionid], 'inputspec.label_file')
baw200.connect(PHASE_2_oneSubjWorkflow[sessionid], 'outputspec.t1_average', FSCROSS_WF[sessionid], 'inputspec.T1_files')
baw200.connect(PHASE_2_oneSubjWorkflow[sessionid], 'outputspec.t2_average', FSCROSS_WF[sessionid], 'inputspec.T2_files')
baw200.connect(PHASE_2_oneSubjWorkflow[sessionid], 'outputspec.outputLabels', FSCROSS_WF[sessionid], 'inputspec.label_file')

from PipeLineFunctionHelpers import GetOnePosteriorImageFromDictionaryFunction
baw200.connect([(PHASE_2_oneSubjWorkflow[sessionid], myLocalFSWF[sessionid],
baw200.connect([(PHASE_2_oneSubjWorkflow[sessionid], FSCROSS_WF[sessionid],
[(('outputspec.posteriorImages', GetOnePosteriorImageFromDictionaryFunction, 'WM'), 'inputspec.wm_prob')])])
baw200.connect(FREESURFER_ID[sessionid], 'FreeSurfer_ID', myLocalFSWF[sessionid], 'inputspec.FreeSurfer_ID')
baw200.connect(FREESURFER_ID[sessionid], 'subj_session_id', FSCROSS_WF[sessionid], 'inputspec.subj_session_id')
### Now define where the final organized outputs should go.
if RunAllFSComponents == True:
FSCROSS_DS_Name="FSCROSS_DS_" + str(subjectid) + "_" + str(sessionid)
FSCROSS_DS[sessionid] = pe.Node(nio.DataSink(), name=FSCROSS_DS_Name)
FSCROSS_DS[sessionid].overwrite = GLOBAL_DATA_SINK_REWRITE
FSCROSS_DS[sessionid].inputs.base_directory = ExperimentBaseDirectoryResults
FSCROSS_DS[sessionid].inputs.regexp_substitutions = [
('/_uid_(?P<myuid>[^/]*)', r'/\g<myuid>')
]
baw200.connect(myLocalFSWF[sessionid], 'outputspec.FreeSurferOutputDirectory', FSCROSS_DS[sessionid], 'FREESURFER52_SUBJECTS.@FreeSurferOutputDirectory')
FSCROSS_DS_Name="FSCROSS_DS_" + str(subjectid) + "_" + str(sessionid)
FSCROSS_DS[sessionid] = pe.Node(nio.DataSink(), name=FSCROSS_DS_Name)
FSCROSS_DS[sessionid].overwrite = GLOBAL_DATA_SINK_REWRITE
FSCROSS_DS[sessionid].inputs.base_directory = ExperimentBaseDirectoryResults
FSCROSS_DS[sessionid].inputs.regexp_substitutions = [ ('/_uid_(?P<myuid>[^/]*)', r'/\g<myuid>') ]
baw200.connect(FSCROSS_WF[sessionid], 'outputspec.full_path_FS_output', FSCROSS_DS[sessionid], 'FREESURFER52_SUBJECTS.@full_path_FS_output')

### Now define where the final organized outputs should go.
FSPREP_DataSink_Name="FREESURFER_PREP_DS_" + str(subjectid) + "_" + str(sessionid)
FSPREP_DataSink[sessionid] = pe.Node(nio.DataSink(), name = FSPREP_DataSink_Name)
FSPREP_DataSink[sessionid].overwrite = GLOBAL_DATA_SINK_REWRITE
FSPREP_DataSink[sessionid].inputs.base_directory = ExperimentBaseDirectoryResults
FREESURFER_PREP_PATTERNS = GenerateOutputPattern(projectid, subjectid, sessionid, FSPREP_DataSink_Name)
FSPREP_DataSink[sessionid].inputs.regexp_substitutions = FREESURFER_PREP_PATTERNS
print "========================="
print "========================="
print "========================="
print FREESURFER_PREP_PATTERNS
print "========================="
print "========================="
print "========================="
baw200.connect(myLocalFSWF[sessionid], 'outputspec.cnr_optimal_image', FSPREP_DataSink[sessionid], 'FREESURFER_PREP.@cnr_optimal_image')
baw200.connect(myLocalFSWF[sessionid], 'outputspec.subj_session_id',
FreeSurferSessionID_MergeNode[subjectid], 'in' + str(FSindex))
baw200.connect(FSCROSS_WF[sessionid], 'outputspec.processed_output_name', FreeSurferSessionID_MergeNode[subjectid], 'in' + str(FSindex))
FSindex += 1

### Now write out the prep image.
FSPREP_DS_Name="FREESURFER_PREP_DS_" + str(subjectid) + "_" + str(sessionid)
FSPREP_DS[sessionid] = pe.Node(nio.DataSink(), name = FSPREP_DS_Name)
FSPREP_DS[sessionid].overwrite = GLOBAL_DATA_SINK_REWRITE
FSPREP_DS[sessionid].inputs.base_directory = ExperimentBaseDirectoryResults
FREESURFER_PREP_PATTERNS = GenerateOutputPattern(projectid, subjectid, sessionid, FSPREP_DS_Name)
FSPREP_DS[sessionid].inputs.regexp_substitutions = FREESURFER_PREP_PATTERNS
baw200.connect(FSCROSS_WF[sessionid], 'outputspec.cnr_optimal_image', FSPREP_DS[sessionid], 'FREESURFER_PREP.@cnr_optimal_image')

#} end of "for sessionid in allSessions:"

#{ Do template building
##HACK : Move later
FSBASE_oneSubjWorkflow = CreateFreeSurferSubjectTemplate(projectid,
FSBASE_WF = CreateFreeSurferSubjectTemplate(projectid,
subjectid,
"FS52_BASE",
CLUSTER_QUEUE,
CLUSTER_QUEUE_LONG,
True,
True,
constructed_FS_SUBJECTS_DIR)
baw200.connect(FreeSurferSessionID_MergeNode[subjectid], 'out',
FSBASE_oneSubjWorkflow, 'inputspec.FreeSurferSession_IDs')

FREESURFER_SUBJ_ID = pe.Node(interface=IdentityInterface(fields=['subjectTemplate_id']),
FREESURFER_SUBJ_ID = pe.Node(interface=IdentityInterface(fields=['base_template_id']),
run_without_submitting=True,
name='99_FSNodeName_' + str(subjectid) + "_template")
FREESURFER_SUBJ_ID.inputs.subjectTemplate_id = str(subjectid) + "_template"
FREESURFER_SUBJ_ID.inputs.base_template_id = str(subjectid) + "_template"

baw200.connect(FREESURFER_SUBJ_ID, 'subjectTemplate_id',
FSBASE_oneSubjWorkflow, 'inputspec.subjectTemplate_id')
baw200.connect(FREESURFER_SUBJ_ID, 'base_template_id', FSBASE_WF, 'inputspec.base_template_id')
baw200.connect(FreeSurferSessionID_MergeNode[subjectid], 'out', FSBASE_WF, 'inputspec.list_all_subj_session_ids')

FSBASE_DS_NAME='FS52_BASE_DS' + str(subjectid)
FSBASE_DataSink[subjectid] = pe.Node(nio.DataSink(), name=FSBASE_DS_NAME)
FSBASE_DataSink[subjectid].overwrite = GLOBAL_DATA_SINK_REWRITE
FREESURFER_TEMP_PATTERNS = GenerateOutputPattern(projectid, subjectid, FSBASE_DS_NAME, '')
FSBASE_DataSink[subjectid].inputs.regexp_substitutions = FREESURFER_TEMP_PATTERNS
baw200.connect(FSBASE_oneSubjWorkflow, 'outputspec.FreeSurferTemplateDir', FSBASE_DataSink[subjectid], 'FREESURFER52_SUBJECTS.@FreeSurferTemplateDir')
FSBASE_DS[subjectid] = pe.Node(nio.DataSink(), name=FSBASE_DS_NAME)
FSBASE_DS[subjectid].overwrite = GLOBAL_DATA_SINK_REWRITE
FSBASE_DS[subjectid].inputs.base_directory = ExperimentBaseDirectoryResults
#FREESURFER_TEMP_PATTERNS = GenerateOutputPattern(projectid, subjectid, sessionid, FSBASE_DS_NAME)
#FSBASE_DS[subjectid].inputs.regexp_substitutions = FREESURFER_TEMP_PATTERNS
FSBASE_DS[subjectid].inputs.regexp_substitutions = [ ('.*/(?P<myuid>_template)', r'/\g<myuid>_template') ]
baw200.connect(FSBASE_WF, 'outputspec.full_path_FS_output', FSBASE_DS[subjectid], 'FREESURFER52_SUBJECTS.@full_path_FS_output')
#}
#{ Do longitudinal analysis
FSLONG_DataSink = dict()
FSLONG_oneSubjWorkflow = dict()
FSLONG_WF = dict()
for sessionid in allSessions:
FSLONG_oneSubjWorkflow[sessionid] = CreateFreeSurferLongitudinalWorkflow(projectid,
FSLONG_WF[sessionid] = CreateFreeSurferLongitudinalWorkflow(projectid,
subjectid,
sessionid,
"FS52_LONG",
Expand All @@ -1147,18 +1138,17 @@ def WorkupT1T2(subjectid, mountPrefix, ExperimentBaseDirectoryCache, ExperimentB
True,
True,
constructed_FS_SUBJECTS_DIR)
baw200.connect(myLocalFSWF[sessionid], 'outputspec.subj_session_id',
FSLONG_oneSubjWorkflow[sessionid], 'inputspec.FreeSurferSession_ID')
baw200.connect(FSBASE_oneSubjWorkflow, 'outputspec.FreeSurferTemplateDir',
FSLONG_oneSubjWorkflow[sessionid], 'inputspec.SingleSubject_ID')
FSLONG_DataSink_Name='_'.join(['FREESURFER_LONG', str(subjectid), str(sessionid)])
FSLONG_DataSink[sessionid] = pe.Node(nio.DataSink(), name=FSLONG_DataSink_Name)
baw200.connect(FSCROSS_WF[sessionid], 'outputspec.processed_output_name', FSLONG_WF[sessionid], 'inputspec.subj_session_id')
baw200.connect(FSBASE_WF, 'outputspec.processed_output_name', FSLONG_WF[sessionid], 'inputspec.base_template_id')

FSLONG_DS='_'.join(['FREESURFER_LONG', str(subjectid), str(sessionid)])
FSLONG_DataSink[sessionid] = pe.Node(nio.DataSink(), name=FSLONG_DS)
FSLONG_DataSink[sessionid].overwrite = GLOBAL_DATA_SINK_REWRITE
FSLONG_DataSink[sessionid].inputs.base_directory = ExperimentBaseDirectoryResults
FREESURFER_LONG_PATTERNS = GenerateOutputPattern(projectid, subjectid, sessionid, FSLONG_DataSink_Name)
FREESURFER_LONG_PATTERNS = GenerateOutputPattern(projectid, subjectid, sessionid, FSLONG_DS)
FSLONG_DataSink[sessionid].inputs.regexp_substitutions = FREESURFER_LONG_PATTERNS

baw200.connect(FSLONG_oneSubjWorkflow[sessionid], 'outputspec.FreeSurferLongitudinalDir', FSLONG_DataSink[sessionid], 'FREESURFER52_SUBJECTS.@longitudinalDirs')
baw200.connect(FSLONG_WF[sessionid], 'outputspec.full_path_FS_output', FSLONG_DataSink[sessionid], 'FREESURFER52_SUBJECTS.@longitudinalDirs')

#} end of "for sessionid in allSessions:"
else:
Expand Down
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