qsiprep.interfaces.dwi_merge module

Handle merging and splitting of DSI files.

class qsiprep.interfaces.dwi_merge.AveragePEPairs(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

• bids_dwi_files (a list of items which are a pathlike object or string representing a file) – List of original (BIDS) dwi files.

• bval_files (a list of items which are a pathlike object or string representing an existing file) – List of bval files.

• bvec_files (a list of items which are a pathlike object or string representing an existing file) – List of bvec files.

• carpetplot_data (a list of items which are a pathlike object or string representing an existing file) – List of carpetplot_data files.

• dwi_files (a list of items which are a pathlike object or string representing a file) – List of dwi files.

• original_bvec_files (a list of items which are a pathlike object or string representing an existing file) – List of original bvec files.

Optional Inputs:

• b0_refs (a list of items which are a pathlike object or string representing a file) – List of b=0 reference images.

• b0_threshold (an integer) – Maximum b=0 value. (Nipype default value: 100)

• denoising_confounds (a list of items which are a pathlike object or string representing an existing file)

• harmonize_b0_intensities (a boolean) – Force scans to have the same mean b=0 intensity. (Nipype default value: True)

• raw_concatenated_files (a list of items which are a pathlike object or string representing a file) – List of raw concatenated images.

• scan_metadata (a dictionary with keys which are any value and with values which are any value) – Dict of metadata for the to-be-combined scans.

• verbose (a boolean) – (Nipype default value: False)

Outputs:

• merged_b0_ref (a pathlike object or string representing an existing file)

• merged_carpetplot_data (a pathlike object or string representing an existing file)

• merged_denoising_confounds (a pathlike object or string representing an existing file)

• merged_metadata (a pathlike object or string representing an existing file)

• merged_raw_bvec (a pathlike object or string representing an existing file)

• merged_raw_concatenated (a pathlike object or string representing an existing file)

• merged_raw_dwi (a pathlike object or string representing an existing file)

• original_images (a list of items which are any value) – The paths to the original images. This will be a list with one element for each volume in the input images.

• out_bval (a pathlike object or string representing a file) – The merged bval file.

• out_bvec (a pathlike object or string representing a file) – The merged bvec file.

• out_dwi (a pathlike object or string representing a file) – The merged dwi image.

class qsiprep.interfaces.dwi_merge.MergeDWIs(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

• bids_dwi_files (a list of items which are a pathlike object or string representing a file) – List of original (BIDS) dwi files.

• bval_files (a list of items which are a pathlike object or string representing an existing file) – List of bval files.

• bvec_files (a list of items which are a pathlike object or string representing an existing file) – List of bvec files.

• dwi_files (a list of items which are a pathlike object or string representing a file) – List of dwi files.

Optional Inputs:

• b0_refs (a list of items which are a pathlike object or string representing a file) – List of b=0 reference images.

• b0_threshold (an integer) – Maximum b=0 value. (Nipype default value: 100)

• carpetplot_data (a list of items which are a pathlike object or string representing an existing file) – List of carpetplot_data files.

• denoising_confounds (a list of items which are a pathlike object or string representing an existing file)

• harmonize_b0_intensities (a boolean) – Force scans to have the same mean b=0 intensity. (Nipype default value: True)

• raw_concatenated_files (a list of items which are a pathlike object or string representing a file) – List of raw concatenated images.

• scan_metadata (a dictionary with keys which are any value and with values which are any value) – Dict of metadata for the to-be-combined scans.

Outputs:

• merged_b0_ref (a pathlike object or string representing an existing file)

• merged_carpetplot_data (a pathlike object or string representing an existing file)

• merged_denoising_confounds (a pathlike object or string representing an existing file)

• merged_metadata (a pathlike object or string representing an existing file)

• merged_raw_bvec (a pathlike object or string representing an existing file)

• merged_raw_dwi (a pathlike object or string representing an existing file)

• original_images (a list of items which are any value) – The paths to the original images. This will be a list with one element for each volume in the input images.

• out_bval (a pathlike object or string representing a file) – The merged bval file.

• out_bvec (a pathlike object or string representing a file) – The merged bvec file.

• out_dwi (a pathlike object or string representing a file) – The merged dwi image.

class qsiprep.interfaces.dwi_merge.MergeFinalConfounds(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

confounds (a pathlike object or string representing an existing file)

Optional Inputs:

• bias_correction_confounds (a list of items which are a pathlike object or string representing an existing file)

• patch2self_correction_confounds (a pathlike object or string representing an existing file)

Outputs:

confounds (a pathlike object or string representing an existing file)

class qsiprep.interfaces.dwi_merge.PhaseToRad(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Convert phase image from arbitrary units (au) to radians.

This method assumes that the phase image’s minimum and maximum values correspond to -pi and pi, respectively, and scales the image to be between 0 and 2*pi.

STATEMENT OF CHANGES: This class is derived from sources licensed under the Apache-2.0 terms, and the code has not been changed.

Notes

The code is derived from https://github.com/nipreps/sdcflows/blob/c6cd42944f4b6d638716ce020ffe51010e9eb58a/ sdcflows/utils/phasemanip.py#L26.

License

ORIGINAL WORK’S ATTRIBUTION NOTICE:

Copyright 2021 The NiPreps Developers <nipreps@gmail.com>

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

We support and encourage derived works from this project, please read about our expectations at

https://www.nipreps.org/community/licensing/

Mandatory Inputs:

phase_file (a pathlike object or string representing an existing file)

Outputs:

phase_file (a pathlike object or string representing an existing file)

class qsiprep.interfaces.dwi_merge.SplitResampledDWIs(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

• bval_file (a pathlike object or string representing an existing file)

• bvec_file (a pathlike object or string representing an existing file)

• confounds (a pathlike object or string representing an existing file)

• dwi_file (a pathlike object or string representing an existing file)

Optional Inputs:

n_images (an integer)

Outputs:

• bval_file_1 (a pathlike object or string representing an existing file)

• bval_file_10 (a pathlike object or string representing an existing file)

• bval_file_100 (a pathlike object or string representing an existing file)

• bval_file_11 (a pathlike object or string representing an existing file)

• bval_file_12 (a pathlike object or string representing an existing file)

• bval_file_13 (a pathlike object or string representing an existing file)

• bval_file_14 (a pathlike object or string representing an existing file)

• bval_file_15 (a pathlike object or string representing an existing file)

• bval_file_16 (a pathlike object or string representing an existing file)

• bval_file_17 (a pathlike object or string representing an existing file)

• bval_file_18 (a pathlike object or string representing an existing file)

• bval_file_19 (a pathlike object or string representing an existing file)

• bval_file_2 (a pathlike object or string representing an existing file)

• bval_file_20 (a pathlike object or string representing an existing file)

• bval_file_21 (a pathlike object or string representing an existing file)

• bval_file_22 (a pathlike object or string representing an existing file)

• bval_file_23 (a pathlike object or string representing an existing file)

• bval_file_24 (a pathlike object or string representing an existing file)

• bval_file_25 (a pathlike object or string representing an existing file)

• bval_file_26 (a pathlike object or string representing an existing file)

• bval_file_27 (a pathlike object or string representing an existing file)

• bval_file_28 (a pathlike object or string representing an existing file)

• bval_file_29 (a pathlike object or string representing an existing file)

• bval_file_3 (a pathlike object or string representing an existing file)

• bval_file_30 (a pathlike object or string representing an existing file)

• bval_file_31 (a pathlike object or string representing an existing file)

• bval_file_32 (a pathlike object or string representing an existing file)

• bval_file_33 (a pathlike object or string representing an existing file)

• bval_file_34 (a pathlike object or string representing an existing file)

• bval_file_35 (a pathlike object or string representing an existing file)

• bval_file_36 (a pathlike object or string representing an existing file)

• bval_file_37 (a pathlike object or string representing an existing file)

• bval_file_38 (a pathlike object or string representing an existing file)

• bval_file_39 (a pathlike object or string representing an existing file)

• bval_file_4 (a pathlike object or string representing an existing file)

• bval_file_40 (a pathlike object or string representing an existing file)

• bval_file_41 (a pathlike object or string representing an existing file)

• bval_file_42 (a pathlike object or string representing an existing file)

• bval_file_43 (a pathlike object or string representing an existing file)

• bval_file_44 (a pathlike object or string representing an existing file)

• bval_file_45 (a pathlike object or string representing an existing file)

• bval_file_46 (a pathlike object or string representing an existing file)

• bval_file_47 (a pathlike object or string representing an existing file)

• bval_file_48 (a pathlike object or string representing an existing file)

• bval_file_49 (a pathlike object or string representing an existing file)

• bval_file_5 (a pathlike object or string representing an existing file)

• bval_file_50 (a pathlike object or string representing an existing file)

• bval_file_51 (a pathlike object or string representing an existing file)

• bval_file_52 (a pathlike object or string representing an existing file)

• bval_file_53 (a pathlike object or string representing an existing file)

• bval_file_54 (a pathlike object or string representing an existing file)

• bval_file_55 (a pathlike object or string representing an existing file)

• bval_file_56 (a pathlike object or string representing an existing file)

• bval_file_57 (a pathlike object or string representing an existing file)

• bval_file_58 (a pathlike object or string representing an existing file)

• bval_file_59 (a pathlike object or string representing an existing file)

• bval_file_6 (a pathlike object or string representing an existing file)

• bval_file_60 (a pathlike object or string representing an existing file)

• bval_file_61 (a pathlike object or string representing an existing file)

• bval_file_62 (a pathlike object or string representing an existing file)

• bval_file_63 (a pathlike object or string representing an existing file)

• bval_file_64 (a pathlike object or string representing an existing file)

• bval_file_65 (a pathlike object or string representing an existing file)

• bval_file_66 (a pathlike object or string representing an existing file)

• bval_file_67 (a pathlike object or string representing an existing file)

• bval_file_68 (a pathlike object or string representing an existing file)

• bval_file_69 (a pathlike object or string representing an existing file)

• bval_file_7 (a pathlike object or string representing an existing file)

• bval_file_70 (a pathlike object or string representing an existing file)

• bval_file_71 (a pathlike object or string representing an existing file)

• bval_file_72 (a pathlike object or string representing an existing file)

• bval_file_73 (a pathlike object or string representing an existing file)

• bval_file_74 (a pathlike object or string representing an existing file)

• bval_file_75 (a pathlike object or string representing an existing file)

• bval_file_76 (a pathlike object or string representing an existing file)

• bval_file_77 (a pathlike object or string representing an existing file)

• bval_file_78 (a pathlike object or string representing an existing file)

• bval_file_79 (a pathlike object or string representing an existing file)

• bval_file_8 (a pathlike object or string representing an existing file)

• bval_file_80 (a pathlike object or string representing an existing file)

• bval_file_81 (a pathlike object or string representing an existing file)

• bval_file_82 (a pathlike object or string representing an existing file)

• bval_file_83 (a pathlike object or string representing an existing file)

• bval_file_84 (a pathlike object or string representing an existing file)

• bval_file_85 (a pathlike object or string representing an existing file)

• bval_file_86 (a pathlike object or string representing an existing file)

• bval_file_87 (a pathlike object or string representing an existing file)

• bval_file_88 (a pathlike object or string representing an existing file)

• bval_file_89 (a pathlike object or string representing an existing file)

• bval_file_9 (a pathlike object or string representing an existing file)

• bval_file_90 (a pathlike object or string representing an existing file)

• bval_file_91 (a pathlike object or string representing an existing file)

• bval_file_92 (a pathlike object or string representing an existing file)

• bval_file_93 (a pathlike object or string representing an existing file)

• bval_file_94 (a pathlike object or string representing an existing file)

• bval_file_95 (a pathlike object or string representing an existing file)

• bval_file_96 (a pathlike object or string representing an existing file)

• bval_file_97 (a pathlike object or string representing an existing file)

• bval_file_98 (a pathlike object or string representing an existing file)

• bval_file_99 (a pathlike object or string representing an existing file)

• bvec_file_1 (a pathlike object or string representing an existing file)

• bvec_file_10 (a pathlike object or string representing an existing file)

• bvec_file_100 (a pathlike object or string representing an existing file)

• bvec_file_11 (a pathlike object or string representing an existing file)

• bvec_file_12 (a pathlike object or string representing an existing file)

• bvec_file_13 (a pathlike object or string representing an existing file)

• bvec_file_14 (a pathlike object or string representing an existing file)

• bvec_file_15 (a pathlike object or string representing an existing file)

• bvec_file_16 (a pathlike object or string representing an existing file)

• bvec_file_17 (a pathlike object or string representing an existing file)

• bvec_file_18 (a pathlike object or string representing an existing file)

• bvec_file_19 (a pathlike object or string representing an existing file)

• bvec_file_2 (a pathlike object or string representing an existing file)

• bvec_file_20 (a pathlike object or string representing an existing file)

• bvec_file_21 (a pathlike object or string representing an existing file)

• bvec_file_22 (a pathlike object or string representing an existing file)

• bvec_file_23 (a pathlike object or string representing an existing file)

• bvec_file_24 (a pathlike object or string representing an existing file)

• bvec_file_25 (a pathlike object or string representing an existing file)

• bvec_file_26 (a pathlike object or string representing an existing file)

• bvec_file_27 (a pathlike object or string representing an existing file)

• bvec_file_28 (a pathlike object or string representing an existing file)

• bvec_file_29 (a pathlike object or string representing an existing file)

• bvec_file_3 (a pathlike object or string representing an existing file)

• bvec_file_30 (a pathlike object or string representing an existing file)

• bvec_file_31 (a pathlike object or string representing an existing file)

• bvec_file_32 (a pathlike object or string representing an existing file)

• bvec_file_33 (a pathlike object or string representing an existing file)

• bvec_file_34 (a pathlike object or string representing an existing file)

• bvec_file_35 (a pathlike object or string representing an existing file)

• bvec_file_36 (a pathlike object or string representing an existing file)

• bvec_file_37 (a pathlike object or string representing an existing file)

• bvec_file_38 (a pathlike object or string representing an existing file)

• bvec_file_39 (a pathlike object or string representing an existing file)

• bvec_file_4 (a pathlike object or string representing an existing file)

• bvec_file_40 (a pathlike object or string representing an existing file)

• bvec_file_41 (a pathlike object or string representing an existing file)

• bvec_file_42 (a pathlike object or string representing an existing file)

• bvec_file_43 (a pathlike object or string representing an existing file)

• bvec_file_44 (a pathlike object or string representing an existing file)

• bvec_file_45 (a pathlike object or string representing an existing file)

• bvec_file_46 (a pathlike object or string representing an existing file)

• bvec_file_47 (a pathlike object or string representing an existing file)

• bvec_file_48 (a pathlike object or string representing an existing file)

• bvec_file_49 (a pathlike object or string representing an existing file)

• bvec_file_5 (a pathlike object or string representing an existing file)

• bvec_file_50 (a pathlike object or string representing an existing file)

• bvec_file_51 (a pathlike object or string representing an existing file)

• bvec_file_52 (a pathlike object or string representing an existing file)

• bvec_file_53 (a pathlike object or string representing an existing file)

• bvec_file_54 (a pathlike object or string representing an existing file)

• bvec_file_55 (a pathlike object or string representing an existing file)

• bvec_file_56 (a pathlike object or string representing an existing file)

• bvec_file_57 (a pathlike object or string representing an existing file)

• bvec_file_58 (a pathlike object or string representing an existing file)

• bvec_file_59 (a pathlike object or string representing an existing file)

• bvec_file_6 (a pathlike object or string representing an existing file)

• bvec_file_60 (a pathlike object or string representing an existing file)

• bvec_file_61 (a pathlike object or string representing an existing file)

• bvec_file_62 (a pathlike object or string representing an existing file)

• bvec_file_63 (a pathlike object or string representing an existing file)

• bvec_file_64 (a pathlike object or string representing an existing file)

• bvec_file_65 (a pathlike object or string representing an existing file)

• bvec_file_66 (a pathlike object or string representing an existing file)

• bvec_file_67 (a pathlike object or string representing an existing file)

• bvec_file_68 (a pathlike object or string representing an existing file)

• bvec_file_69 (a pathlike object or string representing an existing file)

• bvec_file_7 (a pathlike object or string representing an existing file)

• bvec_file_70 (a pathlike object or string representing an existing file)

• bvec_file_71 (a pathlike object or string representing an existing file)

• bvec_file_72 (a pathlike object or string representing an existing file)

• bvec_file_73 (a pathlike object or string representing an existing file)

• bvec_file_74 (a pathlike object or string representing an existing file)

• bvec_file_75 (a pathlike object or string representing an existing file)

• bvec_file_76 (a pathlike object or string representing an existing file)

• bvec_file_77 (a pathlike object or string representing an existing file)

• bvec_file_78 (a pathlike object or string representing an existing file)

• bvec_file_79 (a pathlike object or string representing an existing file)

• bvec_file_8 (a pathlike object or string representing an existing file)

• bvec_file_80 (a pathlike object or string representing an existing file)

• bvec_file_81 (a pathlike object or string representing an existing file)

• bvec_file_82 (a pathlike object or string representing an existing file)

• bvec_file_83 (a pathlike object or string representing an existing file)

• bvec_file_84 (a pathlike object or string representing an existing file)

• bvec_file_85 (a pathlike object or string representing an existing file)

• bvec_file_86 (a pathlike object or string representing an existing file)

• bvec_file_87 (a pathlike object or string representing an existing file)

• bvec_file_88 (a pathlike object or string representing an existing file)

• bvec_file_89 (a pathlike object or string representing an existing file)

• bvec_file_9 (a pathlike object or string representing an existing file)

• bvec_file_90 (a pathlike object or string representing an existing file)

• bvec_file_91 (a pathlike object or string representing an existing file)

• bvec_file_92 (a pathlike object or string representing an existing file)

• bvec_file_93 (a pathlike object or string representing an existing file)

• bvec_file_94 (a pathlike object or string representing an existing file)

• bvec_file_95 (a pathlike object or string representing an existing file)

• bvec_file_96 (a pathlike object or string representing an existing file)

• bvec_file_97 (a pathlike object or string representing an existing file)

• bvec_file_98 (a pathlike object or string representing an existing file)

• bvec_file_99 (a pathlike object or string representing an existing file)

• dwi_file_1 (a pathlike object or string representing an existing file)

• dwi_file_10 (a pathlike object or string representing an existing file)

• dwi_file_100 (a pathlike object or string representing an existing file)

• dwi_file_11 (a pathlike object or string representing an existing file)

• dwi_file_12 (a pathlike object or string representing an existing file)

• dwi_file_13 (a pathlike object or string representing an existing file)

• dwi_file_14 (a pathlike object or string representing an existing file)

• dwi_file_15 (a pathlike object or string representing an existing file)

• dwi_file_16 (a pathlike object or string representing an existing file)

• dwi_file_17 (a pathlike object or string representing an existing file)

• dwi_file_18 (a pathlike object or string representing an existing file)

• dwi_file_19 (a pathlike object or string representing an existing file)

• dwi_file_2 (a pathlike object or string representing an existing file)

• dwi_file_20 (a pathlike object or string representing an existing file)

• dwi_file_21 (a pathlike object or string representing an existing file)

• dwi_file_22 (a pathlike object or string representing an existing file)

• dwi_file_23 (a pathlike object or string representing an existing file)

• dwi_file_24 (a pathlike object or string representing an existing file)

• dwi_file_25 (a pathlike object or string representing an existing file)

• dwi_file_26 (a pathlike object or string representing an existing file)

• dwi_file_27 (a pathlike object or string representing an existing file)

• dwi_file_28 (a pathlike object or string representing an existing file)

• dwi_file_29 (a pathlike object or string representing an existing file)

• dwi_file_3 (a pathlike object or string representing an existing file)

• dwi_file_30 (a pathlike object or string representing an existing file)

• dwi_file_31 (a pathlike object or string representing an existing file)

• dwi_file_32 (a pathlike object or string representing an existing file)

• dwi_file_33 (a pathlike object or string representing an existing file)

• dwi_file_34 (a pathlike object or string representing an existing file)

• dwi_file_35 (a pathlike object or string representing an existing file)

• dwi_file_36 (a pathlike object or string representing an existing file)

• dwi_file_37 (a pathlike object or string representing an existing file)

• dwi_file_38 (a pathlike object or string representing an existing file)

• dwi_file_39 (a pathlike object or string representing an existing file)

• dwi_file_4 (a pathlike object or string representing an existing file)

• dwi_file_40 (a pathlike object or string representing an existing file)

• dwi_file_41 (a pathlike object or string representing an existing file)

• dwi_file_42 (a pathlike object or string representing an existing file)

• dwi_file_43 (a pathlike object or string representing an existing file)

• dwi_file_44 (a pathlike object or string representing an existing file)

• dwi_file_45 (a pathlike object or string representing an existing file)

• dwi_file_46 (a pathlike object or string representing an existing file)

• dwi_file_47 (a pathlike object or string representing an existing file)

• dwi_file_48 (a pathlike object or string representing an existing file)

• dwi_file_49 (a pathlike object or string representing an existing file)

• dwi_file_5 (a pathlike object or string representing an existing file)

• dwi_file_50 (a pathlike object or string representing an existing file)

• dwi_file_51 (a pathlike object or string representing an existing file)

• dwi_file_52 (a pathlike object or string representing an existing file)

• dwi_file_53 (a pathlike object or string representing an existing file)

• dwi_file_54 (a pathlike object or string representing an existing file)

• dwi_file_55 (a pathlike object or string representing an existing file)

• dwi_file_56 (a pathlike object or string representing an existing file)

• dwi_file_57 (a pathlike object or string representing an existing file)

• dwi_file_58 (a pathlike object or string representing an existing file)

• dwi_file_59 (a pathlike object or string representing an existing file)

• dwi_file_6 (a pathlike object or string representing an existing file)

• dwi_file_60 (a pathlike object or string representing an existing file)

• dwi_file_61 (a pathlike object or string representing an existing file)

• dwi_file_62 (a pathlike object or string representing an existing file)

• dwi_file_63 (a pathlike object or string representing an existing file)

• dwi_file_64 (a pathlike object or string representing an existing file)

• dwi_file_65 (a pathlike object or string representing an existing file)

• dwi_file_66 (a pathlike object or string representing an existing file)

• dwi_file_67 (a pathlike object or string representing an existing file)

• dwi_file_68 (a pathlike object or string representing an existing file)

• dwi_file_69 (a pathlike object or string representing an existing file)

• dwi_file_7 (a pathlike object or string representing an existing file)

• dwi_file_70 (a pathlike object or string representing an existing file)

• dwi_file_71 (a pathlike object or string representing an existing file)

• dwi_file_72 (a pathlike object or string representing an existing file)

• dwi_file_73 (a pathlike object or string representing an existing file)

• dwi_file_74 (a pathlike object or string representing an existing file)

• dwi_file_75 (a pathlike object or string representing an existing file)

• dwi_file_76 (a pathlike object or string representing an existing file)

• dwi_file_77 (a pathlike object or string representing an existing file)

• dwi_file_78 (a pathlike object or string representing an existing file)

• dwi_file_79 (a pathlike object or string representing an existing file)

• dwi_file_8 (a pathlike object or string representing an existing file)

• dwi_file_80 (a pathlike object or string representing an existing file)

• dwi_file_81 (a pathlike object or string representing an existing file)

• dwi_file_82 (a pathlike object or string representing an existing file)

• dwi_file_83 (a pathlike object or string representing an existing file)

• dwi_file_84 (a pathlike object or string representing an existing file)

• dwi_file_85 (a pathlike object or string representing an existing file)

• dwi_file_86 (a pathlike object or string representing an existing file)

• dwi_file_87 (a pathlike object or string representing an existing file)

• dwi_file_88 (a pathlike object or string representing an existing file)

• dwi_file_89 (a pathlike object or string representing an existing file)

• dwi_file_9 (a pathlike object or string representing an existing file)

• dwi_file_90 (a pathlike object or string representing an existing file)

• dwi_file_91 (a pathlike object or string representing an existing file)

• dwi_file_92 (a pathlike object or string representing an existing file)

• dwi_file_93 (a pathlike object or string representing an existing file)

• dwi_file_94 (a pathlike object or string representing an existing file)

• dwi_file_95 (a pathlike object or string representing an existing file)

• dwi_file_96 (a pathlike object or string representing an existing file)

• dwi_file_97 (a pathlike object or string representing an existing file)

• dwi_file_98 (a pathlike object or string representing an existing file)

• dwi_file_99 (a pathlike object or string representing an existing file)

• source_file_1 (a string)

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class qsiprep.interfaces.dwi_merge.StackConfounds(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

in_files (a list of items which are a pathlike object or string representing an existing file)

Optional Inputs:

• axis (0 or 1) – (Nipype default value: 0)

• out_file (a pathlike object or string representing a file)

Outputs:

confounds_file (a pathlike object or string representing a file) – The stacked confound data.

qsiprep.interfaces.dwi_merge.angle_between(v1, v2)

Returns the angle in degrees between vectors ‘v1’ and ‘v2’:: >>> angle_between((1, 0, 0), (0, 1, 0)) 90.0 >>> angle_between((1, 0, 0), (1, 0, 0)) 0.0 >>> angle_between((1, 0, 0), (-1, 0, 0)) 180.0

qsiprep.interfaces.dwi_merge.average_bvec(bvec1, bvec2)

qsiprep.interfaces.dwi_merge.average_carpetplots(carpet_list, image_pairs)

Averages carpetplot data for display when pe pairs are averaged.

Reminder: incoming data is a dict of {“carpetplot”: [[one image’s slice scores],

[next image’s slice scores], … [last image’s slice scores]]}

and the image_pairs should be a n x 2 matrix where the columns are the first image index and second image index.

qsiprep.interfaces.dwi_merge.average_image_pairs(image_pairs, image_paths, rotated_bvecs, bvals, confounds_tsvs, raw_concatenated_files, carpetplots, verbose=False)

Create 4D series of averaged images, gradients, and confounds

qsiprep.interfaces.dwi_merge.combine_bvals(bvals, output_file='restacked.bval')

Load, merge and save fsl-style bvals files.

qsiprep.interfaces.dwi_merge.combine_bvecs(bvecs, output_file='restacked.bvec')

Load, merge and save fsl-style bvecs files.

qsiprep.interfaces.dwi_merge.combine_metadata(scan_list, metadata_dict, merge_method='first')

Create a merged metadata dictionary.

Most importantly, combine the slice timings in some way.

Parameters:

• scan_list (list) – List of BIDS inputs in the order in which they’ll be concatenated

• medadata_dict (dict) – Mapping keys (values in scan_list) to BIDS metadata dictionaries

• merge_method (str) – How to combine the metadata when multiple scans are being concatenated. If “first” the metadata from the first scan is selected. Someday other methods like “average” may be added.

Returns:

metadata – A BIDS metadata dictionary

Return type:

dict

qsiprep.interfaces.dwi_merge.combined_bval_array(bval_files)

qsiprep.interfaces.dwi_merge.combined_bvec_array(bvec_files)

qsiprep.interfaces.dwi_merge.create_provenance_dataframe(bids_sources, harmonized_niis, b0_means, harmonization_corrections)

qsiprep.interfaces.dwi_merge.find_image_pairs(original_bvecs, bvals, assignments)

qsiprep.interfaces.dwi_merge.get_nvols(img)

Returns the number of volumes in a 3/4D nifti file.

qsiprep.interfaces.dwi_merge.get_worst(values1, values2)

finds the highest magnitude value per index in values1, values2

qsiprep.interfaces.dwi_merge.harmonize_b0s(dwi_files, bvals, b0_threshold, do_harmonization)

Find the mean intensity of b=0 images in a dwi file and calculate corrections.

Parameters:

• dwi_files (list of str) – List of paths to dwi Nifti files that will be concatenated

• bvals (list of str) – List of paths to bval files corresponding to the files in dwi_files

• b0_threshold (int) – maximum b values for an image to be considered a b=0

• do_harmonization (bool) – Apply a correction to each image so that their mean b=0 images are equal

Returns:

• to_concat (list of NiftiImage objects) – List of NiftiImage objects to be concatenated. May have been harmonized. Same length as the input dwi_files.

• b0_means (list of floats) – The mean b=0 intensity of each dwi series. Same length as the input dwi_files.

• corrections (list of floats) – The correction that would be applied to each image to harmonize their b=0’s. Same length as the input dwi_files. If do_harmonization is False, this will be a list of ones.

qsiprep.interfaces.dwi_merge.subset_bvals(bval_file, indices, out_bval_file)

qsiprep.interfaces.dwi_merge.subset_bvecs(bvec_file, indices, out_bvec_file)

qsiprep.interfaces.dwi_merge.unit_vector(vector)

Returns the unit vector of the vector.