qsirecon.interfaces.dsi_studio module

class qsirecon.interfaces.dsi_studio.AggregateAutoTrackResults(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Optional Inputs:

• expected_bundles (a list of items which are a string)

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

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

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

Outputs:

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

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

• found_bundle_names (a list of items which are a string)

class qsirecon.interfaces.dsi_studio.AutoTrack(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: CommandLine

Wrapped executable: dsi_studio --action=atk.

Mandatory Inputs:

fib_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: --source=%s.

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

• export_trk (a boolean) – Maps to a command-line argument: --export_trk=%d. (Nipype default value: True)

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

• num_threads (an integer) – Maps to a command-line argument: --thread_count=%d. (Nipype default value: 1)

• otsu_threshold (a float) – The ratio of otsu threshold to derive default anisotropy threshold. Maps to a command-line argument: --otsu_threshold=%.10f.

• output_dir (a string) – Forces DSI Studio to write results in cwd. Maps to a command-line argument: %s. (Nipype default value: cwd)

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

• smoothing (a float) – Smoothing. Maps to a command-line argument: --smoothing=%.10f.

• template (an integer) – Must be 0 for autotrack. Maps to a command-line argument: --template=%d. (Nipype default value: 0)

• tip_iterations (an integer) – Topologically-informed pruning iterations. Maps to a command-line argument: --tip_iteration=%d.

• tolerance (a string) –

  The tolerance for the bundle recognition. The unit is in mm. Multiple values

  can be assigned using comma separator. A larger value may include larger track variation but also subject to more false results.

  Maps to a command-line argument: --tolerance=%s.

• track_id (a string) –

  Specify the id number or the name of the bundle. The id can be found in

  /atlas/ICBM152/HCP1065.tt.gz.txt . This text file is included in DSI Studio package (For Mac, right-click on dsi_studio_64.app to find content). You can specify partial name of the bundle:

  example: for tracking left and right arcuate fasciculus, assign –track_id=0,1 or –track_id=arcuate (DSI Studio will find bundles with names containing “arcuate”, case insensitive)

  example: for tracking left and right arcuate and cingulum, assign -track_id=0,1,2,3 or -track_id=arcuate,cingulum.

  Maps to a command-line argument: --track_id=%s. (Nipype default value: Fasciculus,Cingulum,Aslant,Corticos,Thalamic_R,Reticular,Optic,Fornix,Corpus)

• track_voxel_ratio (a float) – The track-voxel ratio for the total number of streamline count. A larger value gives better mapping with the expense of computation time. Maps to a command-line argument: --track_voxel_ratio=%.2f. (Nipype default value: 2.0)

• trk_format (‘trk.gz’ or ‘tt.gz’) – Maps to a command-line argument: --trk_format=%s. (Nipype default value: trk.gz)

• yield_rate (a float) – This rate will be used to terminate tracking early if DSI Studio find the fiber trackings is not generating results. Maps to a command-line argument: --yield_rate=%.10f.

Outputs:

• dsistudiotemplate (a string) – DSI Studio’s name for the template used for registration.

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

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

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

class qsirecon.interfaces.dsi_studio.ChenAutoTrack(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: AutoTrack

Wrapped executable: dsi_studio_chen --action=atk.

Mandatory Inputs:

fib_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: --source=%s.

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

• export_trk (a boolean) – Maps to a command-line argument: --export_trk=%d. (Nipype default value: True)

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

• num_threads (an integer) – Maps to a command-line argument: --thread_count=%d. (Nipype default value: 1)

• otsu_threshold (a float) – The ratio of otsu threshold to derive default anisotropy threshold. Maps to a command-line argument: --otsu_threshold=%.10f.

• output_dir (a string) – Forces DSI Studio to write results in cwd. Maps to a command-line argument: %s. (Nipype default value: cwd)

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

• smoothing (a float) – Smoothing. Maps to a command-line argument: --smoothing=%.10f.

• template (an integer) – Must be 0 for autotrack. Maps to a command-line argument: --template=%d. (Nipype default value: 0)

• tip_iterations (an integer) – Topologically-informed pruning iterations. Maps to a command-line argument: --tip_iteration=%d.

• tolerance (a string) –

  The tolerance for the bundle recognition. The unit is in mm. Multiple values

  can be assigned using comma separator. A larger value may include larger track variation but also subject to more false results.

  Maps to a command-line argument: --tolerance=%s.

• track_id (a string) –

  Specify the id number or the name of the bundle. The id can be found in

  /atlas/ICBM152/HCP1065.tt.gz.txt . This text file is included in DSI Studio package (For Mac, right-click on dsi_studio_64.app to find content). You can specify partial name of the bundle:

  example: for tracking left and right arcuate fasciculus, assign –track_id=0,1 or –track_id=arcuate (DSI Studio will find bundles with names containing “arcuate”, case insensitive)

  example: for tracking left and right arcuate and cingulum, assign -track_id=0,1,2,3 or -track_id=arcuate,cingulum.

  Maps to a command-line argument: --track_id=%s. (Nipype default value: Fasciculus,Cingulum,Aslant,Corticos,Thalamic_R,Reticular,Optic,Fornix,Corpus)

• track_voxel_ratio (a float) – The track-voxel ratio for the total number of streamline count. A larger value gives better mapping with the expense of computation time. Maps to a command-line argument: --track_voxel_ratio=%.2f. (Nipype default value: 2.0)

• trk_format (‘trk.gz’ or ‘tt.gz’) – Maps to a command-line argument: --trk_format=%s. (Nipype default value: trk.gz)

• yield_rate (a float) – This rate will be used to terminate tracking early if DSI Studio find the fiber trackings is not generating results. Maps to a command-line argument: --yield_rate=%.10f.

Outputs:

• dsistudiotemplate (a string) – DSI Studio’s name for the template used for registration.

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

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

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

class qsirecon.interfaces.dsi_studio.DSIStudioAtlasGraph(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Produce one connectivity matrix per atlas based on DSI Studio tractography

Mandatory Inputs:

input_fib (a pathlike object or string representing an existing file) – Maps to a command-line argument: --source=%s.

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• atlas_configs (a dictionary with keys which are any value and with values which are any value) – Atlas configs for atlases to run connectivity for. Keys are atlas names and values are dictionaries with the following keys: ‘dwi_resolution_file’ and ‘labels’. ‘dwi_resolution_file’ is the parcellation file in the same resolution as the DWI data. ‘labels’ is the parcellation labels file.

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

• atlas_name (a string)

• connectivity (a string) – Maps to a command-line argument: --connectivity=%s.

• connectivity_type (a string) – Maps to a command-line argument: --connectivity_type=%s.

• connectivity_value (a string) – Maps to a command-line argument: --connectivity_value=%s.

• environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

• fa_threshold (a float) – Maps to a command-line argument: --fa_threshold=%.2f.

• fiber_count (an integer) – Maps to a command-line argument: --fiber_count=%d. Mutually exclusive with inputs: seed_count.

• initial_dir (0 or 1 or 2) – Maps to a command-line argument: --initial_dir=%d.

• interpo_angle (a float) – Maps to a command-line argument: --interpo_angle=%.2f.

• interpolation (0 or 1 or 2) – Maps to a command-line argument: --interpolation=%d.

• max_length (an integer) – Maps to a command-line argument: --max_length=%d.

• min_length (an integer) – Maps to a command-line argument: --min_length=%d.

• num_threads (an integer) – Maps to a command-line argument: --thread_count=%d. (Nipype default value: 1)

• random_seed (a boolean) – Maps to a command-line argument: --random_seed=1.

• seed_count (an integer) – Maps to a command-line argument: --seed_count=%d. Mutually exclusive with inputs: fiber_count.

• seed_file (a pathlike object or string representing an existing file) – Specify the seeding file. Supported file format includes text, Analyze, and nifti files. Maps to a command-line argument: --seed=%s.

• seed_plan (0 or 1) – Maps to a command-line argument: --seed_plan=%d.

• smoothing (a float) – Maps to a command-line argument: --smoothing=%.2f.

• step_size (a float) – Maps to a command-line argument: --step_size=%.2f.

• to_export (a string) – Maps to a command-line argument: --export=%s.

• trk_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: --tract=%s.

• turning_angle (a float) – Maps to a command-line argument: --turning_angle=%.2f.

Outputs:

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

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

class qsirecon.interfaces.dsi_studio.DSIStudioConnectivityMatrix(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: CommandLine

Wrapped executable: dsi_studio --action=ana.

Mandatory Inputs:

input_fib (a pathlike object or string representing an existing file) – Maps to a command-line argument: --source=%s.

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

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

• atlas_name (a string)

• connectivity (a string) – Maps to a command-line argument: --connectivity=%s.

• connectivity_type (a string) – Maps to a command-line argument: --connectivity_type=%s.

• connectivity_value (a string) – Maps to a command-line argument: --connectivity_value=%s.

• environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

• fa_threshold (a float) – Maps to a command-line argument: --fa_threshold=%.2f.

• fiber_count (an integer) – Maps to a command-line argument: --fiber_count=%d. Mutually exclusive with inputs: seed_count.

• initial_dir (0 or 1 or 2) – Maps to a command-line argument: --initial_dir=%d.

• interpo_angle (a float) – Maps to a command-line argument: --interpo_angle=%.2f.

• interpolation (0 or 1 or 2) – Maps to a command-line argument: --interpolation=%d.

• max_length (an integer) – Maps to a command-line argument: --max_length=%d.

• min_length (an integer) – Maps to a command-line argument: --min_length=%d.

• num_threads (an integer) – Maps to a command-line argument: --thread_count=%d. (Nipype default value: 1)

• random_seed (a boolean) – Maps to a command-line argument: --random_seed=1.

• seed_count (an integer) – Maps to a command-line argument: --seed_count=%d. Mutually exclusive with inputs: fiber_count.

• seed_file (a pathlike object or string representing an existing file) – Specify the seeding file. Supported file format includes text, Analyze, and nifti files. Maps to a command-line argument: --seed=%s.

• seed_plan (0 or 1) – Maps to a command-line argument: --seed_plan=%d.

• smoothing (a float) – Maps to a command-line argument: --smoothing=%.2f.

• step_size (a float) – Maps to a command-line argument: --step_size=%.2f.

• to_export (a string) – Maps to a command-line argument: --export=%s.

• trk_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: --tract=%s.

• turning_angle (a float) – Maps to a command-line argument: --turning_angle=%.2f.

Outputs:

connectivity_matfile (a string or os.PathLike object referring to an existing file)

class qsirecon.interfaces.dsi_studio.DSIStudioCreateSrc(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: CommandLine

Wrapped executable: dsi_studio --action=src.

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bvec_convention (‘DIPY’ or ‘FSL’) – Convention used for bvecs. FSL assumes LAS+ no matter image orientation. (Nipype default value: DIPY)

• environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

• grad_dev (a pathlike object or string representing an existing file) – Gradient deviation file. Maps to a command-line argument: #%s (position: -1).

• input_b_table_file (a pathlike object or string representing an existing file) – Text file containing q-space sampling (DSI Studio format). Maps to a command-line argument: --b_table=%s.

• input_bvals_file (a pathlike object or string representing an existing file) – Text file containing b values. Maps to a command-line argument: --bval=%s.

• input_bvecs_file (a pathlike object or string representing an existing file) – Text file containing b vectors (FSL format). Maps to a command-line argument: --bvec=%s.

• input_dicom_dir (a pathlike object or string representing an existing file) – Directory with DICOM data from only the dwi. Maps to a command-line argument: --source=%s.

• input_nifti_file (a pathlike object or string representing a file) – DWI Nifti file. Maps to a command-line argument: --source=%s.

• output_src (a pathlike object or string representing a file) – Output file (.src.gz). Maps to a command-line argument: --output=%s.

• recursive (a boolean) – Search for DICOM files recursively. Maps to a command-line argument: --recursive=1.

• subject_id (a string)

• test_trait (a boolean)

Outputs:

output_src (a pathlike object or string representing a file) – Output file (.src.gz).

class qsirecon.interfaces.dsi_studio.DSIStudioExport(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: CommandLine

Wrapped executable: dsi_studio --action=exp.

Mandatory Inputs:

• input_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: --source=%s.

• to_export (a string) – Maps to a command-line argument: --export=%s.

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

Outputs:

• ad_file (a pathlike object or string representing a file) – Exported scalar nifti.

• dti_fa_file (a pathlike object or string representing a file) – Exported scalar nifti.

• gfa_file (a pathlike object or string representing a file) – Exported scalar nifti.

• ha_file (a pathlike object or string representing a file) – Exported scalar nifti.

• image0_file (a pathlike object or string representing a file) – Exported files.

• iso_file (a pathlike object or string representing a file) – Exported scalar nifti.

• md_file (a pathlike object or string representing a file) – Exported scalar nifti.

• nrdi02L_file (a pathlike object or string representing a file) – Exported scalar nifti.

• nrdi04L_file (a pathlike object or string representing a file) – Exported scalar nifti.

• nrdi06L_file (a pathlike object or string representing a file) – Exported scalar nifti.

• qa_file (a pathlike object or string representing a file) – Exported scalar nifti.

• rd1_file (a pathlike object or string representing a file) – Exported scalar nifti.

• rd2_file (a pathlike object or string representing a file) – Exported scalar nifti.

• rd_file (a pathlike object or string representing a file) – Exported scalar nifti.

• rdi_file (a pathlike object or string representing a file) – Exported scalar nifti.

• txx_file (a pathlike object or string representing a file) – Exported scalar nifti.

• txy_file (a pathlike object or string representing a file) – Exported scalar nifti.

• txz_file (a pathlike object or string representing a file) – Exported scalar nifti.

• tyy_file (a pathlike object or string representing a file) – Exported scalar nifti.

• tyz_file (a pathlike object or string representing a file) – Exported scalar nifti.

• tzz_file (a pathlike object or string representing a file) – Exported scalar nifti.

class qsirecon.interfaces.dsi_studio.DSIStudioGQIReconstruction(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: CommandLine

Wrapped executable: dsi_studio --action=rec --method=4.

Mandatory Inputs:

input_src_file (a pathlike object or string representing an existing file) – DSI Studio src file. Maps to a command-line argument: --source=%s.

Optional Inputs:

• align_acpc (a boolean) – Rotate image volume to align ap-pc. Maps to a command-line argument: --align_acpc=%d. (Nipype default value: False)

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• check_btable (0 or 1) – Check if btable matches nifti orientation (not foolproof). Maps to a command-line argument: --check_btable=%d. (Nipype default value: 0)

• dti_no_high_b (a boolean) – Specify whether the construction of DTI should ignore high b-value (b>1500). Maps to a command-line argument: --dti_no_high_b=%d. (Nipype default value: True)

• environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

• grad_dev (a pathlike object or string representing an existing file) – Gradient deviation file. Maps to a command-line argument: #%s (position: -1).

• mask (a pathlike object or string representing an existing file) – Volume to mask brain voxels. Maps to a command-line argument: --mask=%s.

• num_threads (an integer) – Maps to a command-line argument: --thread_count=%d. (Nipype default value: 1)

• odf_order (8 or 4 or 5 or 6 or 10 or 12 or 16 or 20) – ODF tesselation order. (Nipype default value: 8)

• other_output (a string) – Additional diffusion metrics to calculate. Maps to a command-line argument: --other_output=%s. (Nipype default value: all)

• output_odf (a boolean) – Include full ODF’s in output. Maps to a command-line argument: --record_odf=1. (Nipype default value: True)

• r2_weighted (a boolean) – Specify whether GQI and QSDR uses r2-weighted to calculate SDF. Maps to a command-line argument: --r2_weighted=%d. (Nipype default value: False)

• ratio_of_mean_diffusion_distance (a float) – Maps to a command-line argument: --param0=%.4f. (Nipype default value: 1.25)

Outputs:

output_fib (a pathlike object or string representing an existing file) – Output File.

class qsirecon.interfaces.dsi_studio.DSIStudioReconstruction(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: CommandLine

Wrapped executable: dsi_studio --action=rec.

Mandatory Inputs:

input_src_file (a pathlike object or string representing an existing file) – DSI Studio src file. Maps to a command-line argument: --source=%s.

Optional Inputs:

• align_acpc (a boolean) – Rotate image volume to align ap-pc. Maps to a command-line argument: --align_acpc=%d. (Nipype default value: False)

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• check_btable (0 or 1) – Check if btable matches nifti orientation (not foolproof). Maps to a command-line argument: --check_btable=%d. (Nipype default value: 0)

• dti_no_high_b (a boolean) – Specify whether the construction of DTI should ignore high b-value (b>1500). Maps to a command-line argument: --dti_no_high_b=%d. (Nipype default value: True)

• environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

• grad_dev (a pathlike object or string representing an existing file) – Gradient deviation file. Maps to a command-line argument: #%s (position: -1).

• hamming_window_len (an integer) – Maps to a command-line argument: --param0=%d.

• mask (a pathlike object or string representing an existing file) – Volume to mask brain voxels. Maps to a command-line argument: --mask=%s.

• num_threads (an integer) – Maps to a command-line argument: --thread_count=%d. (Nipype default value: 1)

• odf_order (8 or 4 or 5 or 6 or 10 or 12 or 16 or 20) – ODF tesselation order. (Nipype default value: 8)

• other_output (a string) – Additional diffusion metrics to calculate. Maps to a command-line argument: --other_output=%s. (Nipype default value: all)

• output_odf (a boolean) – Include full ODF’s in output. Maps to a command-line argument: --record_odf=1. (Nipype default value: True)

• r2_weighted (a boolean) – Specify whether GQI and QSDR uses r2-weighted to calculate SDF. Maps to a command-line argument: --r2_weighted=%d. (Nipype default value: False)

Outputs:

output_fib (a pathlike object or string representing an existing file) – Output File.

class qsirecon.interfaces.dsi_studio.DSIStudioTracking(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: CommandLine

Wrapped executable: dsi_studio --action=trk.

Mandatory Inputs:

input_fib (a pathlike object or string representing an existing file) – Maps to a command-line argument: --source=%s.

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

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

• atlas_name (a string)

• connectivity (a string) – Maps to a command-line argument: --connectivity=%s.

• connectivity_type (a string) – Maps to a command-line argument: --connectivity_type=%s.

• connectivity_value (a string) – Maps to a command-line argument: --connectivity_value=%s.

• end (a pathlike object or string representing an existing file) – Maps to a command-line argument: --end=%s.

• end2 (a pathlike object or string representing an existing file) – Maps to a command-line argument: --end2=%s.

• environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

• fa_threshold (a float) – Maps to a command-line argument: --fa_threshold=%.2f.

• fiber_count (an integer) – Maps to a command-line argument: --fiber_count=%d. Mutually exclusive with inputs: seed_count.

• initial_dir (0 or 1 or 2) – Maps to a command-line argument: --initial_dir=%d.

• interpo_angle (a float) – Maps to a command-line argument: --interpo_angle=%.2f.

• interpolation (0 or 1 or 2) – Maps to a command-line argument: --interpolation=%d.

• max_length (an integer) – Maps to a command-line argument: --max_length=%d.

• min_length (an integer) – Maps to a command-line argument: --min_length=%d.

• num_threads (an integer) – Maps to a command-line argument: --thread_count=%d. (Nipype default value: 1)

• output_trk (a string) – Output file (trk.gz). Maps to a command-line argument: --output=%s.

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

• random_seed (a boolean) – Maps to a command-line argument: --random_seed=1.

• roa (a pathlike object or string representing an existing file) – Maps to a command-line argument: --roa=%s.

• roi (a pathlike object or string representing an existing file) – Maps to a command-line argument: --roi=%s.

• roi2 (a pathlike object or string representing an existing file) – Maps to a command-line argument: --roi2=%s.

• seed_count (an integer) – Maps to a command-line argument: --seed_count=%d. Mutually exclusive with inputs: fiber_count.

• seed_file (a pathlike object or string representing an existing file) – Specify the seeding file. Supported file format includes text, Analyze, and nifti files. Maps to a command-line argument: --seed=%s.

• seed_plan (0 or 1) – Maps to a command-line argument: --seed_plan=%d.

• smoothing (a float) – Maps to a command-line argument: --smoothing=%.2f.

• step_size (a float) – Maps to a command-line argument: --step_size=%.2f.

• ter (a pathlike object or string representing an existing file) – Maps to a command-line argument: --ter=%s.

• to_export (a string) – Maps to a command-line argument: --export=%s.

• trk_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: --tract=%s.

• turning_angle (a float) – Maps to a command-line argument: --turning_angle=%.2f.

Outputs:

• connectivity_matrices (a list of items which are any value)

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

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

• output_trk (a string) – Output file (trk.gz). Maps to a command-line argument: --output=%s.

class qsirecon.interfaces.dsi_studio.FixDSIStudioExportHeader(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

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

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

Outputs:

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

qsirecon.interfaces.dsi_studio.btable_from_bvals_bvecs(bval_file, bvec_file, output_file)

Create a b-table from DIPY-style bvals/bvecs.

Assuming these come from qsirecon they will be in LPS+, which is the same convention as DSI Studio’s btable.

qsirecon.interfaces.dsi_studio.stat_txt_to_df(stat_txt_file, bundle_name)