FreeSurfer MRI Format Conversion (mri_convert)¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Converts between neuroimaging file formats (DICOM, NIfTI, MGH/MGZ, ANALYZE, etc.) with optional resampling and conforming.
Modality: Any neuroimaging volume format.
Typical Use: Converting DICOM to NIfTI, conforming images to FreeSurfer standards.
Key Parameters¶
--conform (resample to 256 cubed at 1mm isotropic), --out_type (output format), -vs (voxel size)
Key Points¶
Use --conform to prepare T1 for FreeSurfer processing. Handles DICOM to NIfTI conversion. Can change voxel size and data type.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
input |
File |
Yes | Input volume file | |
output |
string |
Yes | Output filename | |
in_type |
string |
No | Input file format (cor, mgh, mgz, minc, analyze, nifti1, nii) | --in_type |
out_type |
string |
No | Output file format (cor, mgh, mgz, minc, analyze, nifti1, nii) | --out_type |
conform |
boolean |
No | Conform to 1mm voxel size in coronal slices | --conform |
conform_min |
boolean |
No | Conform to minimum voxel direction size | --conform_min |
conform_size |
double |
No | Conform to specified voxel size in mm | --conform_size |
vox_size |
string |
No | Output voxel size (x y z) in mm | --voxsize |
out_orientation |
string |
No | Output orientation (e.g., RAS, LPS) | --out_orientation |
in_orientation |
string |
No | Input orientation (e.g., RAS, LPS) | --in_orientation |
resample_type |
enum |
No | Interpolation method | --resample_type |
reslice_like |
File |
No | Reslice to match template geometry | --reslice_like |
apply_transform |
File |
No | Apply transformation (xfm or m3z) | --apply_transform |
apply_inverse_transform |
File |
No | Apply inverse transformation | --apply_inverse_transform |
crop |
string |
No | Crop to 256 around center (x y z) | --crop |
cropsize |
string |
No | Crop to specified size (dx dy dz) | --cropsize |
frame |
int |
No | Keep specified 0-based frame number | --frame |
mid_frame |
boolean |
No | Keep only middle frame | --mid-frame |
nskip |
int |
No | Skip first n frames | --nskip |
ndrop |
int |
No | Drop last n frames | --ndrop |
out_data_type |
enum |
No | Output data type | --out_data_type |
fwhm |
double |
No | Smooth input volume by FWHM in mm | --fwhm |
no_scale |
boolean |
No | Do not rescale values for COR | --no_scale |
force_ras |
boolean |
No | Use default when orientation info absent | --force_ras_good |
split |
boolean |
No | Split output frames into separate files | --split |
ascii |
boolean |
No | Save output as ASCII | --ascii |
read_only |
boolean |
No | Read-only mode (no output written) | --read_only |
Accepted Input Extensions¶
- input:
.mgz,.mgh,.nii,.nii.gz,.img,.hdr,.mnc - reslice_like:
.mgz,.mgh,.nii,.nii.gz - apply_transform:
.xfm,.m3z,.lta - apply_inverse_transform:
.xfm,.m3z,.lta
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
converted |
File |
$(inputs.output)* |
log |
File |
mri_convert.log |
Output Extensions¶
- converted:
.mgz,.mgh,.nii,.nii.gz
Enum Options¶
resample_type: interpolate, weighted, nearest, sinc, 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¶
- Structural MRI > FreeSurfer > Surface Reconstruction
- Utilities > FreeSurfer > Format Conversion