dwi_f99#

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

dwi_f99 [... processing options]

Run FSL's F99 registration for macaque diffusion/structural data.

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

Warning

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

Parameters

--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). Note that previous data is deleted before the run, so in the case of a failed command run, previous results are lost.
--logfolder (str, default ''):: The path to the folder where logs are to be stored, if other than default.
--diffusion_folder (str, default '<sessions_folder>/<session>/NHP/dMRI'):: The path to the diffusion folder holding the dtifit results.

Output files

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

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

Examples

qunex dwi_f99 \
    --sessionsfolder="/data/macaque_study/sessions" \
    --sessions="hilary,jane" \
    --overwrite=no \
    --parsessions=2

QuNex documentation