FreeSurfer Diffusion Post-Registration Processing¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Post-registration processing for diffusion MRI data as part of the TRACULA tractography pipeline.
Modality: Registered diffusion MRI data within FreeSurfer/TRACULA directory structure.
Typical Use: Part of TRACULA pipeline for automated tractography.
Key Parameters¶
--s (subject), --reg (registration method: bbr or manual)
Key Points¶
Part of TRACULA pipeline. Handles diffusion-to-structural registration refinement. Usually called by trac-all.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
input |
File |
Yes | Input diffusion volume | --i |
output |
string |
Yes | Output filename | --o |
reg |
File |
No | Registration file (DWI to anatomy) | --reg |
xfm |
File |
No | Transformation matrix | --xfm |
ref |
File |
No | Reference volume | --ref |
mask |
File |
No | Brain mask | --mask |
subject |
string |
No | FreeSurfer subject name | --s |
interp |
enum |
No | Interpolation method | --interp |
noresample |
boolean |
No | Do not resample | --noresample |
Accepted Input Extensions¶
- input:
.mgz,.mgh,.nii,.nii.gz - reg:
.dat,.lta - xfm:
.xfm,.lta,.dat - ref:
.mgz,.mgh,.nii,.nii.gz - mask:
.mgz,.mgh,.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
out_file |
File |
$(inputs.output)* |
log |
File |
dmri_postreg.log |
Output Extensions¶
- out_file:
.mgz,.mgh,.nii,.nii.gz
Enum Options¶
interp: nearest, trilin, cubic
Docker Tags¶
Available versions: latest, 8.1.0, 8.0.0, 7.2.0, 7.3.0, 7.3.1, 7.3.2, 7.4.1, 7.1.1, 6.0
Categories¶
- Diffusion MRI > FreeSurfer > Diffusion