AFNI Atlas Location Query (whereami)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Reports anatomical atlas labels for given coordinates or identifies regions in multiple atlases simultaneously.
Modality: MNI or Talairach coordinates, or labeled dataset.
Typical Use: Identifying anatomical locations of activation peaks.
Key Parameters¶
-coord_file (coordinate file), -atlas (atlas name), -lpi/-rai (coordinate system)
Key Points¶
Queries multiple atlases at once by default. Coordinates must match atlas space.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
coord |
double[] |
No | Brain location in mm (x y z) | |
coord_file |
File |
No | Input coordinates from file | -coord_file |
lpi |
boolean |
No | Input uses LPI/SPM orientation | -lpi |
rai |
boolean |
No | Input uses RAI/DICOM orientation | -rai |
atlas |
string |
No | Specify atlas(es) to use | -atlas |
show_atlas_code |
boolean |
No | Show integer code to area label map | -show_atlas_code |
show_atlas_region |
string |
No | Show region using symbolic notation (Atlas:Side:Area) | -show_atlas_region |
mask_atlas_region |
string |
No | Create mask for specified region | -mask_atlas_region |
prefix |
string |
No | Output prefix for mask datasets | -prefix |
space |
string |
No | Template space (MNI, TLRC, etc.) | -space |
dset |
File |
No | Determine template space from reference dataset | -dset |
max_areas |
int |
No | Maximum distinct areas to report | -max_areas |
max_search_radius |
double |
No | Maximum search distance | -max_search_radius |
min_prob |
double |
No | Minimum probability threshold for probabilistic atlases | -min_prob |
bmask |
File |
No | Report overlap of non-zero voxels with atlas regions | -bmask |
omask |
File |
No | Report each ROI overlap separately | -omask |
classic |
boolean |
No | Standard output format | -classic |
tab |
boolean |
No | Tab-delimited output format | -tab |
Accepted Input Extensions¶
- coord_file:
.1D,.txt - dset:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - bmask:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - omask:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
output |
stdout |
|
mask_output |
File |
$(inputs.prefix)+tlrc.*, $(inputs.prefix)+orig.*, $(inputs.prefix).nii* |
log |
File |
whereami.log |
Output Extensions¶
- output:
.txt - mask_output:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK,.nii,.nii.gz
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Utilities > AFNI > ROI Utilities