dwi_xtract
dwi_xtract#
- qx_utilities.processing.fsl.dwi_xtract(sinfo, options, overwrite=False, thread=0)#
dwi_xtract [... processing options]
fslx [... processing options]
This command executes FSL's XTRACT (cross-species tractography) command. It can be used to automatically extract a set of carefully dissected tracts in humans and macaques. It can also be used to define one's own tractography protocols where all the user needs to do is to define a set of masks in standard space (e.g. MNI152).
Warning
Successful completion of FSL's bedpostx processing (dwi_bedpostx_gpu command in QuNex) is required. For macaques FSL F99 registration is also required (dwi_f99 command in QuNex).
Parameters
- --batchfile (str, default ''):
The batch.txt file with all the sessions information.
- --sessionsfolder (str, default '.'):
The path to the study/sessions folder, where the imaging data is supposed to go.
- --parsessions (int, default 1):
How many sessions to run in parallel.
- --overwrite (str, default 'no'):
Whether to overwrite existing data (yes) or not (no).
- --logfolder (str, default ''):
The path to the folder where runlogs and comlogs are to be stored, if other than default.
- --log (str, default 'keep'):
Whether to keep ("keep") or remove ("remove") the temporary logs once jobs are completed. When a comma or pipe ("|") separated list is given, the log will be created at the first provided location and then linked or copied to other locations. The valid locations are:
"study" (for the default: <study>/processing/logs/comlogs location)
"session" (for <sessionid>/logs/comlogs)
"hcp" (for <hcp_folder>/logs/comlogs)
"<path>" (for an arbitrary directory).
- --species (str, default 'human'):
Species: human or macaque.
- --nogpu (flag, optional):
Do not use the GPU version, this flag is not set by default.
- --xtract_list (str, default ''):
Comma separated list of tract names.
- --xtract_structures (str, default ''):
Path to structures file (format: <tractName> per line OR format: <tractName> [samples=1], 1 means 1000, '#' to skip lines).
- --xtract_protocols (str, default $FSLDIR/data/xtract_data/<species>):
Protocols folder (all masks in same standard space).
- --xtract_stdwarp (str, default detailed below):
Standard2diff and Diff2standard transforms. Default for humans is set to session's: [acpc_dc2standard.nii.gz and standard2acpc_dc.nii.gz], for macaques warp fields from F99 registration command (dwi_f99) are used by default.
- --xtract_resolution (int, default detailed below):
Output resolution in mm. Default is the same as in the protocols folder unless --native is used.
- --xtract_ptx_options (str, default detailed below):
Pass extra probtrackx2 options as a text file to override defaults (e.g. --steplength=0.2). For humans it defaults to '', for macaques it defaults to '$TOOLS/python/qx_utilities/templates/nhp/ptx_options'.
- --xtract_native (flag, optional):
Run tractography in native (diffusion) space. This flag is not set by default.
- --xtract_ref (str, default ''):
Reference image ("<refimage> <diff2ref> <ref2diff>") for running tractography in reference space, Diff2Reference and Reference2Diff transforms.
Output files
The results of this step will be present in the dMRI/NHP/xtract folder in the sessions's root:
study └─ sessions ├─ session1 | └─ dMRI | └─ NHP | └─ xtract └─ session2 └─ dMRI └─ NHP └─ xtract
Examples
qunex dwi_xtract \ --sessionsfolder="/data/macaque_study/sessions" \ --batchfile="/data/example_study/processing/batch.txt" \ --species="human" \ --overwrite=yes
qunex dwi_xtract \ --sessionsfolder="/data/macaque_study/sessions" \ --batchfile="hilary,jane" \ --species="macaque" \ --overwrite=no \ --parsessions=2