Class: Reconstruction
- Includes:
- DefaultRecon
- Defined in:
- lib/rpipe.rb
Overview
A class for performing initial reconstruction of both functional and anatomical MRI scan acquisitions. Uses AFNI to convert from dicoms to 3D or 4D nifti files, initial volume stripping, and slice timing correction. Currently, supports dicoms or P-Files.
Constant Summary collapse
- VOLUME_SKIP =
number of volumes to strip from beginning of functional scans.
3
Constants inherited from JobStep
Instance Attribute Summary collapse
-
#scans ⇒ Object
Returns the value of attribute scans.
-
#volume_skip ⇒ Object
Returns the value of attribute volume_skip.
Attributes inherited from JobStep
#collision_policy, #libdir, #origdir, #procdir, #rawdir, #spmdir, #statsdir, #step, #subid
Instance Method Summary collapse
-
#initialize(workflow_spec, recon_spec) ⇒ Reconstruction
constructor
Instances are initialized with a properly configured hash containing all the information needed to drive reconstruction tasks.
Methods included from DefaultRecon
#build_physionoise_run_spec, #build_retroicor_cmd, #create_physiosnoise_regressors, #generate_physiospec, #recon_visit, #reconstruct_scan, #run_retroicor, #slice_time_correct, #strip_leading_volumes
Methods inherited from JobStep
#check_instance_vars, #default_spmdir, #include_custom_methods, #job_requires, #setup_directory, #validate_existence_of
Constructor Details
#initialize(workflow_spec, recon_spec) ⇒ Reconstruction
Instances are initialized with a properly configured hash containing all the information needed to drive reconstruction tasks. This hash is normally generated with a Pipe object.
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# File 'lib/rpipe.rb', line 152 def initialize(workflow_spec, recon_spec) super(workflow_spec, recon_spec) raise ScriptError, "At least one scan must be specified." if @scans.nil? @volume_skip = recon_spec['volume_skip'] || VOLUME_SKIP job_requires 'rawdir', 'origdir', 'scans' end |
Instance Attribute Details
#scans ⇒ Object
Returns the value of attribute scans.
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# File 'lib/rpipe.rb', line 148 def scans @scans end |
#volume_skip ⇒ Object
Returns the value of attribute volume_skip.
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# File 'lib/rpipe.rb', line 148 def volume_skip @volume_skip end |