qsiprep.interfaces.dsi_studio module

class qsiprep.interfaces.dsi_studio.DSIStudioBTable(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)

Optional Inputs:

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

Outputs:

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

class qsiprep.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.

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

• 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 qsiprep.interfaces.dsi_studio.DSIStudioFibQC(from_file=None, resource_monitor=None, **inputs)

Bases: DSIStudioQC

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: {})

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

• src_file (a pathlike object or string representing an existing file) – DSI Studio fib[.gz] file. Maps to a command-line argument: %s.

Outputs:

qc_txt (a pathlike object or string representing an existing file) – Text file with QC measures.

ext = '.fib.gz'

class qsiprep.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_fibers (an integer) – Number of fiber populations estimated at each voxel. Maps to a command-line argument: --num_fiber=%d. (Nipype default value: 3)

• 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 tessellation 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)

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

Outputs:

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

class qsiprep.interfaces.dsi_studio.DSIStudioMergeQC(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

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

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

Outputs:

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

class qsiprep.interfaces.dsi_studio.DSIStudioQC(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Outputs:

qc_txt (a pathlike object or string representing an existing file) – Text file with QC measures.

class qsiprep.interfaces.dsi_studio.DSIStudioSrcQC(from_file=None, resource_monitor=None, **inputs)

Bases: DSIStudioQC

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: {})

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

• src_file (a pathlike object or string representing an existing file) – DSI Studio src[.gz] file. Maps to a command-line argument: %s.

Outputs:

qc_txt (a pathlike object or string representing an existing file) – Text file with QC measures.

ext = '.src.gz'

qsiprep.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 qsiprep they will be in LPS+, which is the same convention as DSI Studio’s btable.

qsiprep.interfaces.dsi_studio.load_fib_qc_file(fname)

qsiprep.interfaces.dsi_studio.load_src_qc_file(fname, prefix='')