FreeSurfer Geometric Transfer Matrix Partial Volume Correction¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Performs partial volume correction for PET data using the geometric transfer matrix method based on high-resolution anatomical segmentation.
Modality: PET volume (3D NIfTI/MGZ) plus FreeSurfer segmentation (aparc+aseg).
Typical Use: Partial volume correction of PET data using anatomical segmentation.
Key Parameters¶
--i (input PET), --seg (segmentation), --reg (registration to anatomy), --psf (point spread function FWHM in mm), --o (output directory)
Key Points¶
Accounts for PET spatial resolution blurring across tissue boundaries. PSF should match scanner resolution (~4-6mm).
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
input |
File |
Yes | Input PET image | --i |
psf |
double |
Yes | Point spread function FWHM (mm) | --psf |
seg |
File |
Yes | Segmentation file | --seg |
output_dir |
string |
Yes | Output directory | --o |
auto_mask_fwhm |
double |
No | Auto-mask smoothing FWHM (mm) | --auto-mask |
auto_mask_thresh |
double |
No | Auto-mask threshold (use with auto_mask_fwhm) | |
reg |
File |
No | Registration file (LTA or reg.dat) | --reg |
regheader |
boolean |
No | Assume registration is identity (header registration) | --regheader |
no_rescale |
boolean |
No | Do not global rescale | --no-rescale |
no_reduce_fov |
boolean |
No | Do not reduce FOV | --no-reduce-fov |
default_seg_merge |
boolean |
No | Use default scheme to merge hemispheres and set tissue types | --default-seg-merge |
ctab_default |
boolean |
No | Use default FreeSurfer color table with tissue types | --ctab-default |
vg_thresh |
double |
No | Volume geometry threshold for registration check | --vg-thresh |
Accepted Input Extensions¶
- input:
.mgz,.mgh,.nii,.nii.gz - seg:
.mgz,.mgh,.nii,.nii.gz - reg:
.lta,.dat
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
output_directory |
Directory |
$(inputs.output_dir) |
gtm_stats |
File |
$(inputs.output_dir)/gtm.stats.dat |
log |
File |
mri_gtmpvc.log |
err_log |
File |
mri_gtmpvc.err.log |
Output Extensions¶
- gtm_stats:
.dat
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¶
- PET > FreeSurfer > PET Processing