fitlins.interfaces.afni module

class fitlins.interfaces.afni.FirstLevelModel(errorts=False, *args, **kwargs)

Bases: fitlins.interfaces.nistats.FirstLevelModel

get_stim_labels()

save_remlfit_results(maps, contrasts, runtime)

Parse the AFNI “bucket” datasets written by 3dREMLfit and subsequently read using nibabel. Save the results to disk according to fitlins expectation. Parameters ———- maps : A dictionary of nibabel.interfaces.brikhead.AFNIImage objects

keyed by output map type Description contrasts : TYPE Description runtime : TYPE Description

contrasts : Object returned by nistats.contrasts.prepare_constrasts runtime : nipype runtime object

save_tsnr(runtime, rbetas, rvars)

class fitlins.interfaces.afni.Pval(**inputs)

Bases: nipype.interfaces.afni.base.AFNICommand

Converts a dataset statistical sub-bricks to p-values, or optionally zscores. All output volumes will be converted to float format, bub-bricks that are not marked as statistical volumes are otherwise unchanged.

For complete details, see the 3dPval Documentation.

>>> from nipype.interfaces import afni
>>> pval = afni.Pval()
>>> pval.inputs.in_file = 'functional.nii'
>>> pval.inputs.out_file = 'output.nii'
>>> pval.cmdline
'3dPval -in_file functional.nii -prefix output.nii'
>>> res = pval.run()  

input_spec

alias of fitlins.interfaces.afni.PvalInputSpec

output_spec

alias of nipype.interfaces.afni.base.AFNICommandOutputSpec

class fitlins.interfaces.afni.PvalInputSpec(**kwargs)

Bases: nipype.interfaces.afni.base.AFNICommandInputSpec

fitlins.interfaces.afni.create_glt_test_info(design, contrasts)

fitlins.interfaces.afni.extract_volume(imgs, idx, intent_name, fname)

fitlins.interfaces.afni.get_afni_design_matrix(design, contrasts, stim_labels, t_r)

Add appropriate metadata to the design matrix and write to file for calling 3dREMLfit. For a description of the target format see https://docs.google.com/document/d/1zpujpZYuleB7HuIFjb2vC4sYXG5M97hJ655ceAj4vE0/edit

designpandas.DataFrame

Matrix containing regressor for model fit.

contrasts : output of nistats.contrasts.prepare_contrasts stim_labels : List of strings specifying model conditions t_r : float

TR in seconds

str

Design matrix with AFNI niml header

fitlins.interfaces.afni.get_afni_intent_info(img)

fitlins.interfaces.afni.get_afni_intent_info_for_subvol(img, idx=0)

fitlins.interfaces.afni.get_glt_rows(wt_arrays)

Generates the appropriate text for generalized linear testing in 3dREMLfit.

wt_arraystuple of np.arrays One of the

Description

TYPE

Description

fitlins.interfaces.afni.load_bucket_by_prefix(tmpdir, prefix)

fitlins.interfaces.afni.parse_afni_ext(nifti_file)

fitlins.interfaces.afni.set_intents(img_list, intent_info)