MRtrix3

Module contents

Input and output specification dicationaries for MRtrix3 analyses.

Submodules

django_mri.analysis.specifications.mrtrix3.bias_correct module

Input and output specification dictionaries for MRtrix’s dwibiascorrect script.

See also

Notes

For more information, see MRtrix3’s dwibiascorrect reference.

django_mri.analysis.specifications.mrtrix3.bias_correct.BIAS_CORRECT_INPUT_SPECIFICATION = {'bias': {'default': 'bias.mif', 'description': 'The output noise map.', 'is_output_path': True, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'bval_scale': {'choices': ['yes', 'no'], 'default': 'yes', 'description': 'Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'grad_file': {'description': 'DWI gradient scheme (MRTrix format). Mutually exclusive with inputs: grad_fsl.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'grad_fsl': {'description': 'DWI gradient scheme (FSL format). Mutually exclusive with inputs: grad_file.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'in_bval': {'description': 'Bvals file in FSL format.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'in_bvec': {'description': 'Bvecs file in FSL format.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'in_file': {'description': 'Input DWI image.', 'is_configuration': False, 'required': True, 'type': <class 'django_mri.models.inputs.scan_input_definition.ScanInputDefinition'>, 'value_attribute': 'mif.__str__'}, 'in_mask': {'description': 'Mask image.', 'type': <class 'django_mri.models.inputs.scan_input_definition.ScanInputDefinition'>, 'value_attribute': 'mif.__str__'}, 'nthreads': {'description': 'Number of threads. if zero, the number of available cpus will be used.', 'type': <class 'django_analyses.models.input.definitions.integer_input_definition.IntegerInputDefinition'>}, 'out_file': {'default': 'bias_corrected.nii.gz', 'description': 'The output denoised DWI image.', 'is_output_path': True, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'use_ants': {'description': 'Use ANTS N4 to estimate the inhomogeneity field. Mutually exclusive with inputs: use_fsl.', 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'use_fsl': {'description': 'Use FSL FAST to estimate the inhomogeneity field. Mutually exclusive with inputs: use_ants.', 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}}

DWIBiasCorrect input specification dictionary.

django_mri.analysis.specifications.mrtrix3.bias_correct.BIAS_CORRECT_OUTPUT_SPECIFICATION = {'bias': {'description': 'The output bias field.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'out_file': {'description': 'The output denoised DWI image.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}}

DWIBiasCorrect output specification dictionary.

django_mri.analysis.specifications.mrtrix.degibbs module

Input and output specification dictionaries for MRtrix’s mrdegibbs script.

See also

Notes

For more information, see MRtrix3’s mrdegibbs reference.

django_mri.analysis.specifications.mrtrix3.degibbs.DEGIBBS_INPUT_SPECIFICATION = {'axes': {'default': [0, 1], 'description': 'Indicate the plane in which the data was acquired (axial = 0,1; coronal = 0,2; sagittal = 1,2).', 'element_type': 'INT', 'type': <class 'django_analyses.models.input.definitions.list_input_definition.ListInputDefinition'>}, 'bval_scale': {'choices': ['yes', 'no'], 'default': 'yes', 'description': 'Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'grad_file': {'description': 'Dw gradient scheme (MRTrix format). Mutually exclusive with inputs: grad_fsl.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'grad_fsl': {'description': 'dw gradient scheme (FSL format). Mutually exclusive with inputs: grad_file.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'in_bval': {'description': 'Bvals file in FSL format.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'in_bvec': {'description': 'Bvecs file in FSL format.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'in_file': {'is_configuration': False, 'required': True, 'type': <class 'django_mri.models.inputs.scan_input_definition.ScanInputDefinition'>, 'value_attribute': 'mif.__str__'}, 'maxW': {'default': 3, 'description': 'Right border of window used for total variation (TV) computation.', 'type': <class 'django_analyses.models.input.definitions.integer_input_definition.IntegerInputDefinition'>}, 'minW': {'default': 1, 'description': 'Left border of window used for total variation (TV) computation.', 'type': <class 'django_analyses.models.input.definitions.integer_input_definition.IntegerInputDefinition'>}, 'nshifts': {'default': 20, 'description': 'Discretization of subpixel spacing.', 'type': <class 'django_analyses.models.input.definitions.integer_input_definition.IntegerInputDefinition'>}, 'nthreads': {'description': 'Number of threads. if zero, the number of available cpus will be used.', 'type': <class 'django_analyses.models.input.definitions.integer_input_definition.IntegerInputDefinition'>}, 'out_file': {'default': 'denoised.mif', 'description': 'The output denoised DWI image.', 'is_output_path': True, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}}

MRDeGibbs input specification.

django_mri.analysis.specifications.mrtrix3.degibbs.DEGIBBS_OUTPUT_SPECIFICATION = {'out_file': {'description': 'The output denoised DWI image.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}}

MRDeGibbs output specification.

django_mri.analysis.specifications.mrtrix.denoise module

Input and output specification dictionaries for MRtrix’s dwidenoise script.

See also

Notes

For more information, see MRtrix3’s dwidenoise reference.

django_mri.analysis.specifications.mrtrix.dwifslpreproc module

Input and output specification dictionaries for MRtrix’s dwifslpreproc script.

See also

Notes

For more information, see MRtrix3’s dwifslpreproc reference.

django_mri.analysis.specifications.mrtrix3.dwifslpreproc.DWIFSLPREPROC_INPUT_SPECIFICATION = {'align_seepi': {'description': 'Achieve alignment between the SE-EPI images used for inhomogeneity field estimation, and the DWIs (more information in Description section)', 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'destination': {'description': 'Run output destination.', 'is_configuration': False, 'is_output_directory': True, 'required': False, 'run_method_input': True, 'type': <class 'django_analyses.models.input.definitions.directory_input_definition.DirectoryInputDefinition'>}, 'eddy_mask': {'description': 'Provide a processing mask to use for eddy, instead of having dwifslpreproc generate one internally using dwi2mask', 'type': <class 'django_analyses.models.input.definitions.file_input_definition.FileInputDefinition'>}, 'eddy_options': {'description': 'Manually provide additional command-line options to the eddy command (provide a string within quotation marks that contains at least one space, even if only passing a single command-line option to eddy)', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'eddy_slspec': {'description': 'Provide a file containing slice groupings for eddy’s slice-to-volume registration', 'type': <class 'django_analyses.models.input.definitions.file_input_definition.FileInputDefinition'>}, 'eddyqc_all': {'description': 'Copy ALL outputs generated by eddy (including images), and the output of eddy_qc (if installed), into an output directory', 'is_output_path': True, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'eddyqc_text': {'description': 'Copy the various text-based statistical outputs generated by eddy, and the output of eddy_qc (if installed), into an output directory', 'is_output_path': True, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'export_grad_fsl': {'description': 'Export the final gradient table in FSL bvecs/bvals format', 'element_type': 'STR', 'type': <class 'django_analyses.models.input.definitions.list_input_definition.ListInputDefinition'>}, 'export_grad_mrtrix': {'description': 'Export the final gradient table in MRtrix format', 'is_output_path': True, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'grad': {'description': 'Provide the diffusion gradient table in MRtrix format', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'grad_fsl': {'description': 'Provide the diffusion gradient table in MRtrix format', 'element_type': 'STR', 'type': <class 'django_analyses.models.input.definitions.list_input_definition.ListInputDefinition'>}, 'json_import': {'description': 'Import image header information from an associated JSON file (may be necessary to determine phase encoding information)', 'type': <class 'django_analyses.models.input.definitions.file_input_definition.FileInputDefinition'>}, 'nocleanup': {'description': 'do not delete intermediate files during script execution, and do not delete scratch directory at script completion.', 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'nthreads': {'description': 'Number of threads. if zero, the number of available cpus will be used.', 'type': <class 'django_analyses.models.input.definitions.integer_input_definition.IntegerInputDefinition'>}, 'pe_dir': {'choices': ['rl', 'lr', 'ap', 'pa', 'is', 'si', '-0', '0', '-1', '1', '-2', '2', 'i', 'i-', 'j', 'j-', 'k', 'k-'], 'description': 'Manually specify the phase encoding direction of the input series', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'readout_time': {'description': 'Manually specify the total readout time of the input series (in seconds)', 'type': <class 'django_analyses.models.input.definitions.float_input_definition.FloatInputDefinition'>}, 'rpe_all': {'description': 'Specify that ALL DWIs have been acquired with opposing phase-encoding', 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'rpe_header': {'description': 'Specify that the phase-encoding information can be found in the image header(s), and that this is the information that the script should use', 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'rpe_none': {'description': 'Specify that no reversed phase-encoding image data is being provided; eddy will perform eddy current and motion correction only', 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'rpe_pair': {'description': 'Specify that a set of images (typically b=0 volumes) will be provided for use in inhomogeneity field estimation only (using the -se_epi option)', 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'scan': {'description': 'Input DWI image.', 'is_configuration': False, 'required': True, 'run_method_input': True, 'type': <class 'django_mri.models.inputs.scan_input_definition.ScanInputDefinition'>, 'value_attribute': 'mif.__str__'}, 'scratch': {'description': 'manually specify the path in which to generate the scratch directory.', 'is_output_path': True, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'se_epi': {'description': 'Provide an additional image series consisting of spin-echo EPI images, which is to be used exclusively by topup for estimating the inhomogeneity field (i.e. it will not form part of the output image series)', 'type': <class 'django_analyses.models.input.definitions.file_input_definition.FileInputDefinition'>}, 'topup_options': {'description': 'Manually provide additional command-line options to the topup command (provide a string within quotation marks that contains at least one space, even if only passing a single command-line option to topup)', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}}

DwiFslPreproc input specification dictionary.

django_mri.analysis.specifications.mrtrix3.dwifslpreproc.DWIFSLPREPROC_OUTPUT_SPECIFICATION = {'eddy_mask': {'description': 'Brain mask used durring eddy currents correction.', 'type': <class 'django_mri.models.outputs.nifti_output_definition.NiftiOutputDefinition'>}, 'out_movement_rms': {'description': 'Summary of the ‘total movement’ in each volume', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'out_outlier_map': {'description': 'Matrix where rows represent volumes and columns represent slices. “0” indicates that scan-slice is not an outlier and “1” indicates that it is.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'out_outlier_n_sqr_stdev_map': {'description': 'Matrix where rows represent volumes and columns represent slices. Values indicate number of standard deivations off the square root of the mean squared difference between observation and prediction is.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'out_outlier_n_stdev_map': {'description': 'Matrix where rows represent volumes and columns represent slices. Values indicate number of standard deviations off the mean difference between observation and prediction is.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'out_outlier_report': {'description': 'Text file with a plain language report on what outlier slices eddy has found.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'out_parameter': {'description': 'Text file with parameters defining the field and movement for each scan.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'out_restricted_movement_rms': {'description': 'Summary of the ‘total movement’ in each volume disregarding translation in the PE direction.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'out_shell_alignment_parameters': {'description': 'Text file containing rigid body movement parameters between the different shells as estimated by a post-hoc mutual information based registration.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'out_shell_pe_translation_parameters': {'description': 'Text file containing translation along the PE-direction between the different shells as estimated by a post-hoc mutual information based registration.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'preprocessed_dwi': {'description': 'The output preprocessed DWI.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}}

DwiFslPreproc output specification dictionary.

django_mri.analysis.specifications.mrtrix.mrconvert module

Input and output specification dictionaries for MRtrix’s mrconvert script.

See also

Notes

For more information, see MRtrix3’s mrconvert reference.

django_mri.analysis.specifications.mrtrix3.mrconvert.MRCONVERT_INPUT_SPECIFICATION = {'axes': {'description': 'specify the axes that will be used', 'element_type': 'INT', 'type': <class 'django_analyses.models.input.definitions.list_input_definition.ListInputDefinition'>}, 'bval_scale': {'choices': ['yes', 'no'], 'default': 'yes', 'description': 'Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'coord': {'description': 'extract data at the specified coordinates', 'element_type': 'FLT', 'type': <class 'django_analyses.models.input.definitions.list_input_definition.ListInputDefinition'>}, 'grad_file': {'description': 'Dw gradient scheme (MRTrix format). Mutually exclusive with inputs: grad_fsl.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'grad_fsl': {'description': '(bvec, bval) DW gradient scheme (FSL format). Mutually exclusive with inputs: grad_file.', 'element_type': 'STR', 'type': <class 'django_analyses.models.input.definitions.list_input_definition.ListInputDefinition'>}, 'in_bval': {'description': 'Bvals file in FSL format.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'in_bvec': {'description': 'Bvecs file in FSL format.', 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'in_file': {'description': 'Input DWI image.', 'is_configuration': False, 'required': True, 'type': <class 'django_mri.models.inputs.nifti_input_definition.NiftiInputDefinition'>}, 'nthreads': {'description': 'Number of threads. if zero, the number of available cpus will be used.', 'type': <class 'django_analyses.models.input.definitions.integer_input_definition.IntegerInputDefinition'>}, 'out_file': {'default': 'denoised.nii.gz', 'description': 'The output denoised DWI image.', 'is_output_path': True, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'scaling': {'description': 'specify the data scaling parameter', 'element_type': 'FLT', 'type': <class 'django_analyses.models.input.definitions.list_input_definition.ListInputDefinition'>}, 'vox': {'description': 'Change the voxel dimensions.', 'element_type': 'FLT', 'type': <class 'django_analyses.models.input.definitions.list_input_definition.ListInputDefinition'>}}

MRConvert input specification dictionary.

django_mri.analysis.specifications.mrtrix3.mrconvert.MRCONVERT_OUTPUT_SPECIFICATION = {'out_file': {'description': 'The output converted image.', 'type': <class 'django_mri.models.outputs.nifti_output_definition.NiftiOutputDefinition'>}}

MRConvert output specification dictionary.