workflows.fmri.spm.preprocess¶
create_DARTEL_template()¶
Create a vbm workflow that generates DARTEL-based template
Example¶
>>> preproc = create_DARTEL_template()
>>> preproc.inputs.inputspec.structural_files = [
... os.path.abspath('s1.nii'), os.path.abspath('s3.nii')]
>>> preproc.inputs.inputspec.template_prefix = 'Template'
>>> preproc.run() # doctest: +SKIP
Inputs:
inputspec.structural_files : structural data to be used to create templates
inputspec.template_prefix : prefix for dartel template
Outputs:
outputspec.template_file : DARTEL template
outputspec.flow_fields : warps from input struct files to the template
Graph¶
![digraph dartel_template{
label="dartel_template";
dartel_template_inputspec[label="inputspec (utility)"];
dartel_template_segment[label="segment (spm)"];
dartel_template_dartel[label="dartel (spm)"];
dartel_template_outputspec[label="outputspec (utility)"];
dartel_template_inputspec -> dartel_template_segment;
dartel_template_inputspec -> dartel_template_dartel;
dartel_template_segment -> dartel_template_dartel;
dartel_template_dartel -> dartel_template_outputspec;
dartel_template_dartel -> dartel_template_outputspec;
}](../../../_images/graphviz-b6b7215d4fff31f963744d2a608ca9f447a1b6f3.png)
create_spm_preproc()¶
Create an spm preprocessing workflow with freesurfer registration and artifact detection.
The workflow realigns and smooths and registers the functional images with the subject’s freesurfer space.
Example¶
>>> preproc = create_spm_preproc()
>>> preproc.base_dir = '.'
>>> preproc.inputs.inputspec.fwhm = 6
>>> preproc.inputs.inputspec.subject_id = 's1'
>>> preproc.inputs.inputspec.subjects_dir = '.'
>>> preproc.inputs.inputspec.functionals = ['f3.nii', 'f5.nii']
>>> preproc.inputs.inputspec.norm_threshold = 1
>>> preproc.inputs.inputspec.zintensity_threshold = 3
Inputs:
inputspec.functionals : functional runs use 4d nifti
inputspec.subject_id : freesurfer subject id
inputspec.subjects_dir : freesurfer subjects dir
inputspec.fwhm : smoothing fwhm
inputspec.norm_threshold : norm threshold for outliers
inputspec.zintensity_threshold : intensity threshold in z-score
Outputs:
outputspec.realignment_parameters : realignment parameter files
outputspec.smoothed_files : smoothed functional files
outputspec.outlier_files : list of outliers
outputspec.outlier_stats : statistics of outliers
outputspec.outlier_plots : images of outliers
outputspec.mask_file : binary mask file in reference image space
outputspec.reg_file : registration file that maps reference image to
freesurfer space
outputspec.reg_cost : cost of registration (useful for detecting misalignment)
Graph¶
![digraph preproc{
label="preproc";
preproc_inputspec[label="inputspec (utility)"];
preproc_realign[label="realign (spm)"];
preproc_smooth[label="smooth (spm)"];
preproc_artdetect[label="artdetect (rapidart)"];
preproc_outputspec[label="outputspec (utility)"];
preproc_inputspec -> preproc_realign;
preproc_inputspec -> preproc_smooth;
preproc_inputspec -> preproc_artdetect;
preproc_inputspec -> preproc_artdetect;
preproc_realign -> preproc_smooth;
preproc_realign -> preproc_artdetect;
preproc_realign -> preproc_artdetect;
preproc_realign -> preproc_outputspec;
preproc_smooth -> preproc_outputspec;
subgraph cluster_preproc_getmask {
label="getmask";
preproc_getmask_inputspec[label="inputspec (utility)"];
preproc_getmask_register[label="register (freesurfer)"];
preproc_getmask_fssource[label="fssource (io)"];
preproc_getmask_threshold[label="threshold (freesurfer)"];
preproc_getmask_transform[label="transform (freesurfer)"];
preproc_getmask_threshold2[label="threshold2 (freesurfer)"];
preproc_getmask_outputspec[label="outputspec (utility)"];
preproc_getmask_inputspec -> preproc_getmask_fssource;
preproc_getmask_inputspec -> preproc_getmask_fssource;
preproc_getmask_inputspec -> preproc_getmask_register;
preproc_getmask_inputspec -> preproc_getmask_register;
preproc_getmask_inputspec -> preproc_getmask_register;
preproc_getmask_inputspec -> preproc_getmask_register;
preproc_getmask_inputspec -> preproc_getmask_transform;
preproc_getmask_inputspec -> preproc_getmask_transform;
preproc_getmask_register -> preproc_getmask_transform;
preproc_getmask_register -> preproc_getmask_outputspec;
preproc_getmask_register -> preproc_getmask_outputspec;
preproc_getmask_fssource -> preproc_getmask_threshold;
preproc_getmask_threshold -> preproc_getmask_transform;
preproc_getmask_transform -> preproc_getmask_threshold2;
preproc_getmask_threshold2 -> preproc_getmask_outputspec;
}
preproc_artdetect -> preproc_outputspec;
preproc_artdetect -> preproc_outputspec;
preproc_artdetect -> preproc_outputspec;
preproc_inputspec -> preproc_getmask_inputspec;
preproc_inputspec -> preproc_getmask_inputspec;
preproc_realign -> preproc_getmask_inputspec;
preproc_getmask_outputspec -> preproc_artdetect;
preproc_getmask_outputspec -> preproc_outputspec;
preproc_getmask_outputspec -> preproc_outputspec;
preproc_getmask_outputspec -> preproc_outputspec;
}](../../../_images/graphviz-45d46ef2964d5d4d32ad81e1674463aa7acc79e5.png)
create_vbm_preproc()¶
Create a vbm workflow that generates DARTEL-based warps to MNI space
Based on: http://www.fil.ion.ucl.ac.uk/~john/misc/VBMclass10.pdf
Example¶
>>> preproc = create_vbm_preproc()
>>> preproc.inputs.inputspec.fwhm = 8
>>> preproc.inputs.inputspec.structural_files = [
... os.path.abspath('s1.nii'), os.path.abspath('s3.nii')]
>>> preproc.inputs.inputspec.template_prefix = 'Template'
>>> preproc.run() # doctest: +SKIP
Inputs:
inputspec.structural_files : structural data to be used to create templates
inputspec.fwhm: single of triplet for smoothing when normalizing to MNI space
inputspec.template_prefix : prefix for dartel template
Outputs:
outputspec.normalized_files : normalized gray matter files
outputspec.template_file : DARTEL template
outputspec.icv : intracranial volume (cc - assuming dimensions in mm)
Graph¶
![digraph vbmpreproc{
label="vbmpreproc";
vbmpreproc_inputspec[label="inputspec (utility)"];
vbmpreproc_calc_icv[label="calc_icv (utility)"];
vbmpreproc_norm2mni[label="norm2mni (spm)"];
vbmpreproc_outputspec[label="outputspec (utility)"];
vbmpreproc_inputspec -> vbmpreproc_norm2mni;
subgraph cluster_vbmpreproc_dartel_template {
label="dartel_template";
vbmpreproc_dartel_template_inputspec[label="inputspec (utility)"];
vbmpreproc_dartel_template_segment[label="segment (spm)"];
vbmpreproc_dartel_template_dartel[label="dartel (spm)"];
vbmpreproc_dartel_template_outputspec[label="outputspec (utility)"];
vbmpreproc_dartel_template_inputspec -> vbmpreproc_dartel_template_segment;
vbmpreproc_dartel_template_inputspec -> vbmpreproc_dartel_template_dartel;
vbmpreproc_dartel_template_segment -> vbmpreproc_dartel_template_dartel;
vbmpreproc_dartel_template_dartel -> vbmpreproc_dartel_template_outputspec;
vbmpreproc_dartel_template_dartel -> vbmpreproc_dartel_template_outputspec;
}
vbmpreproc_calc_icv -> vbmpreproc_outputspec;
vbmpreproc_norm2mni -> vbmpreproc_outputspec;
vbmpreproc_inputspec -> vbmpreproc_dartel_template_inputspec;
vbmpreproc_inputspec -> vbmpreproc_dartel_template_inputspec;
vbmpreproc_dartel_template_outputspec -> vbmpreproc_norm2mni;
vbmpreproc_dartel_template_outputspec -> vbmpreproc_norm2mni;
vbmpreproc_dartel_template_segment -> vbmpreproc_norm2mni;
vbmpreproc_dartel_template_segment -> vbmpreproc_calc_icv;
vbmpreproc_dartel_template_outputspec -> vbmpreproc_outputspec;
}](../../../_images/graphviz-0c12623d78109433ba3249d943ca9472408a0f04.png)