Python Pipeline.recon方法代码示例

本文整理汇总了Python中pipeline.Pipeline.recon方法的典型用法代码示例。如果您正苦于以下问题：Python Pipeline.recon方法的具体用法？Python Pipeline.recon怎么用？Python Pipeline.recon使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类pipeline.Pipeline的用法示例。

在下文中一共展示了Pipeline.recon方法的6个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: SPMJob

# 需要导入模块: from pipeline import Pipeline [as 别名]
# 或者: from pipeline.Pipeline import recon [as 别名]
            StudyVariables.statsTemplateStatsDir,
            StudyVariables.statsTemplateOnsetsDir,
        ],
        StudyVariables.statsTemplateRuns,
        fieldmap=StudyVariables.statsTemplateFM,
    )
    stats_job = SPMJob(subjStatsJob, stats_template_identity, pipe.config["spm_version"])
    print "Replacing Stats SPM Identity in subject job "
    print stats_job
    stats_job.replaceIdentity(subj_stats_identity)


current = os.getcwd()
os.chdir(pipe.working_preprocdir)
if options.recon:
    pipe.recon(StudyVariables.studyName, subjFunctionalFormat)
    if os.path.exists(subid + "_assetRun1.nii"):
        pipe.remove_discdacqs(subid + "_assetRun1.nii", 2)
    if os.path.exists(subid + "_assetRun2.nii"):
        pipe.remove_discdacqs(subid + "_assetRun2.nii", 2)
    if os.path.exists(subid + "_assetRest195.nii"):
        pipe.remove_discdacqs(subid + "_assetRest195.nii", 32)
    if os.path.exists(subid + "_assetRest165.nii"):
        pipe.remove_discdacqs(subid + "_assetRest165.nii", 2)
if options.stc:
    pipe.stc(subjFunctionalFormat)
if options.realign:
    pipe.realign(subjRealignJob)
if options.motioncheck:
    pipe.motionCheck(MOTION_THRESHOLD)
if options.calcderivs:

开发者ID:brainmap，项目名称:WADRC-fMRI-Pipeline，代码行数:33，代码来源:preproc-ries.aware.visit1.py

示例2: SPMJobIdentity

# 需要导入模块: from pipeline import Pipeline [as 别名]
# 或者: from pipeline.Pipeline import recon [as 别名]
    print StudyVariables.statsTemplateSubid
    # make and change stats job instance
    stats_template_identity = SPMJobIdentity (
        StudyVariables.statsTemplateSubid,
        [StudyVariables.statsTemplatePreprocDir, StudyVariables.statsTemplateStatsDir, StudyVariables.statsTemplateOnsetsDir],
        StudyVariables.statsTemplateRuns,
        fieldmap=StudyVariables.statsTemplateFM
    )
    stats_job = SPMJob(subjStatsJob, stats_template_identity)
    print "Replacing Stats SPM Identity in subject job "; print stats_job
    stats_job.replaceIdentity(subj_stats_identity)


current = os.getcwd()
os.chdir(pipe.working_preprocdir)
if options.recon: pipe.recon(StudyVariables.studyName, subjFunctionalFormat)
if options.stc: pipe.stc(subjFunctionalFormat)
if options.realign: pipe.realign(subjRealignJob)
if options.motioncheck: pipe.motionCheck(MOTION_THRESHOLD)
if options.calcderivs: pipe.calcDerivs()
if options.fmap and subjHasFmap: pipe.fieldMap()
if options.normalize: pipe.normSmooth(subjNormJob)
if options.moveLocalFiles: pipe.moveLocalFilesToNetwork()

os.chdir(pipe.statsdir)
if options.stats: pipe.stats1L(subjStatsJob)
os.chdir(current)

开发者ID:brainmap，项目名称:WADRC-fMRI-Pipeline，代码行数:29，代码来源:preproc-johnson.tbi-va.visit1.py

示例3: SPMJob

# 需要导入模块: from pipeline import Pipeline [as 别名]
# 或者: from pipeline.Pipeline import recon [as 别名]
        StudyVariables.statsTemplateRuns,
        fieldmap=StudyVariables.statsTemplateFM
    )
    stats_job = SPMJob(subjStatsJob, stats_template_identity)
    print "Replacing Stats SPM Identity in subject job "; print stats_job
    stats_job.replaceIdentity(subj_stats_identity)


current = os.getcwd()
os.chdir(pipe.working_preprocdir)
if options.recon:
    # If we are to do a reconstruction, check to see if the subject had
    # ref.dat files in the subject csv.  If so, pass them in to the pipe reconstruction,
    # otherwise don't.
    if subjVisitVars.has_key('refdat_files'):
        pipe.recon(StudyVariables.studyName, StudyVariables.studyFunctionalFormat, subjVisitVars['tasks'], subjVisitVars['pfiles'], subjVisitVars['refdat_files'])
    else:
        pipe.recon(StudyVariables.studyName, StudyVariables.studyFunctionalFormat,subjVisitVars['tasks'], subjVisitVars['pfiles'] )
    if os.path.exists(subid + '_assetRun1.nii'): pipe.remove_discdacqs(subid + '_assetRun1.nii', 2)
    if os.path.exists(subid + '_assetRun2.nii'): pipe.remove_discdacqs(subid + '_assetRun2.nii', 2)
    if os.path.exists(subid + '_assetRest195.nii'): pipe.remove_discdacqs(subid + '_assetRest195.nii', 32)
    if os.path.exists(subid + '_assetRest165.nii'): pipe.remove_discdacqs(subid + '_assetRest165.nii', 2)
if options.stc: pipe.stc(subjFunctionalFormat)
if options.realign: pipe.realign(subjRealignJob)
if options.motioncheck: pipe.motionCheck(MOTION_THRESHOLD)
if options.calcderivs: pipe.calcDerivs()
if options.fmap and subjHasFmap: pipe.fieldMap()
if options.normalize: pipe.normSmooth(subjNormJob)
if options.moveLocalFiles: pipe.moveLocalFilesToNetwork()

if options.stats:

开发者ID:brainmap，项目名称:WADRC-fMRI-Pipeline，代码行数:33，代码来源:preproc-johnson.alz.snodsw.visit2.py

示例4: Pipeline

# 需要导入模块: from pipeline import Pipeline [as 别名]
# 或者: from pipeline.Pipeline import recon [as 别名]
print str % ('ALZ2.studyName',StudyVariables.studyName)
print str % ('subjRealignJob',subjRealignJob)
print str % ('MOTION_THRESHOLD',MOTION_THRESHOLD)
print str % ('subjNormJob',subjNormJob)
print str % ('subjStatsJob',subjStatsJob)
print str % ('statstasks',statstasks)

# make a pipe, run it.
pipe = Pipeline(subid, subjRawDir, subjAnatDir, subjPreprocDir, subjStatsDir)
pipe.checkSetup()
if options.recon:
    # If we are to do a reconstruction, check to see if the subject had
    # ref.dat files in the subject csv.  If so, pass them in to the pipe reconstruction,
    # otherwise don't.
    if subjVisitVars.has_key('refdat_files'):
        pipe.recon(subjVisitVars['tasks'], subjVisitVars['pfiles'], StudyVariables.studyName, subjVisitVars['refdat_files'])
    else:
        pipe.recon(subjVisitVars['tasks'], subjVisitVars['pfiles'], StudyVariables.studyName)
if options.stc: pipe.stc()
if options.realign: pipe.realign(subjRealignJob)
if options.motioncheck: pipe.motionCheck(MOTION_THRESHOLD)
if options.calcderivs: pipe.calcDerivs()
if subjHasFmap and options.fmap: pipe.fieldMap()
if options.normalize: pipe.normSmooth(subjNormJob)
if options.stats: pipe.stats1L(subjStatsJob)

开发者ID:brainmap，项目名称:WADRC-fMRI-Pipeline，代码行数:27，代码来源:preproc-johnson.alz.visit2.adaptrecogwithoutrest.py

示例5: SPMJobIdentity

# 需要导入模块: from pipeline import Pipeline [as 别名]
# 或者: from pipeline.Pipeline import recon [as 别名]
    stats_template_identity = SPMJobIdentity (
        ALZ1.statsTemplateSubid,
        [ALZ1.statsTemplatePreprocDir, ALZ1.statsTemplateStatsDir, ALZ1.statsTemplateOnsetsDir],
        ALZ1.statsTemplateRuns,
        fieldmap=ALZ1.statsTemplateFM
    )
    stats_job = SPMJob(subjStatsJob, stats_template_identity)
    stats_job.replaceIdentity(subj_stats_identity)





# make a pipe, run it.
pipe = Pipeline(subid, subjRawDir, subjAnatDir, subjPreprocDir, subjStatsDir)
pipe.checkSetup()
if options.recon: pipe.recon(subjVisitVars['tasks'], subjVisitVars['pfiles'], ALZ1.studyName)
if options.stc: pipe.stc()
if options.realign: pipe.realign(subjRealignJob)
if options.motioncheck: pipe.motionCheck(MOTION_THRESHOLD)
if options.calcderivs: pipe.calcDerivs()
if subjHasFmap and options.fmap: pipe.fieldMap()
if options.normalize: pipe.normSmooth(subjNormJob)
if options.stats: pipe.stats1L(subjStatsJob)

开发者ID:brainmap，项目名称:WADRC-fMRI-Pipeline，代码行数:26，代码来源:preproc_alz1.py

示例6: SPMJobIdentity

# 需要导入模块: from pipeline import Pipeline [as 别名]
# 或者: from pipeline.Pipeline import recon [as 别名]
print str % ('ALZ2.studyName',ALZ2.studyName)
print str % ('subjRealignJob',subjRealignJob)
print str % ('MOTION_THRESHOLD',MOTION_THRESHOLD)
print str % ('subjNormJob',subjNormJob)
print str % ('subjStatsJob',subjStatsJob)
print str % ('statstasks',statstasks)
"""

# make a pipe, run it.
pipe.checkSetup()
current = os.getcwd()
os.chdir(pipe.working_preprocdir)
if options.recon:
    print str % ("subjVisitVars['tasks']",subjVisitVars['tasks'])
    print str % ("subjVisitVars['pfiles']",subjVisitVars['pfiles'])
    print pipe.recon(StudyVariables.studyName, 'pfiles', subjVisitVars['tasks'], subjVisitVars['pfiles'])
if options.stc: pipe.stc()
if options.realign:
    print subjRealignJob, StudyVariables.realignJob
    print str % ("subjVisitVars['tasks']",subjVisitVars['tasks'])
    print str % ("subjVisitVars['pfiles']",subjVisitVars['pfiles'])
    if not os.path.exists(subjRealignJob) and StudyVariables.realignJob:
        shutil.copy(StudyVariables.realignJob, subjRealignJob)
        # making a job instance for the template realign job and changing its identity
        realign_template_identity = SPMJobIdentity (
            StudyVariables.realignTemplateSubid,
            [StudyVariables.realignTemplatePreprocDir],
            StudyVariables.realignTemplateRuns,
            fieldmap=StudyVariables.realignTemplateFM
        )
        realign_job = SPMJob(subjRealignJob, realign_template_identity)

开发者ID:brainmap，项目名称:WADRC-fMRI-Pipeline，代码行数:33，代码来源:preproc_alz2.py

注：本文中的pipeline.Pipeline.recon方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。