qx_utilities.processing.fsl.dwi_f99(sinfo, options, overwrite=False, thread=0)#

dwi_f99 [... processing options]

f99 [... processing options]

This command executes FSL's F99 script for registering your own diffusion or structural data to the F99 atlas. This atlas is used when processing macaque data.


To use this command, successful completion of FSL's dtifit processing (dwi_dtifit command in QuNex) is required.


--batchfile (str, default ''):

The batch.txt file with all the sessions information.

--sessions (str, default ''):

A list of sessions to process.

--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).

Output files

The results of this step will be present in the dMRI/NHP/F99reg folder in the sessions's root:

└─ sessions
   ├─ session1
   |  └─ dMRI
   |    └─ NHP
   |      └─ F99reg
   └─ session2
      └─ dMRI
        └─ NHP
          └─ F99reg


qunex dwi_f99 \
    --sessionsfolder="/data/macaque_study/sessions" \
    --sessions="hilary,jane" \
    --overwrite=no \