Allen Brain Atlas Annotation

Allen Brain Atlas Annotation & ROI Extraction

Overview

The AllenBrainAtlas/atlas/ directory contains the annotation label definitions and MATLAB scripts for extracting regions of interest (ROIs) from the normalized Allen Brain Atlas. These tools map Allen Brain Atlas (ABA) numerical IDs to named brain regions and generate ROI-specific NIfTI volumes used in downstream fMRI analysis.

Directory Structure

AllenBrainAtlas/atlas/
├── doAllROIextract.m        # Batch ROI extraction from atlas
├── doOneROIExtract.m        # Single ROI extraction
├── newLabel.txt             # ROI label definitions (194 regions, revised 2021)
├── newLabel 2.txt           # ROI label definitions (original 2017 version)
├── ROIlabel.xlsm            # Excel workbook with ROI label reference
├── ABA_ROI.nii              # Original ABA ROI volume (not tracked in git)
├── NormalizedAnno2.nii      # Normalized annotation volume (not tracked in git)
├── atlas.nii                # Atlas volume (not tracked in git)
├── newAtlas_roi.nii          # Extracted ROI atlas (not tracked in git)
├── newatlas.nii              # Alternative atlas output (not tracked in git)
└── PVT.nii                   # Paraventricular thalamus ROI (not tracked in git)

Annotation Label File (newLabel.txt)

Format

The label file is a comma-separated text file with the following columns:

ID, ROIname, ROIs, ROI name from Allen Brain Atlas

Column	Description
ID	Primary Allen Brain Atlas structure ID
ROIname	Abbreviated region name used in analysis
ROIs	Array of sub-structure ABA IDs grouped under this region (e.g., [303 311 451])
ROI name from Allen Brain Atlas	Full anatomical name from ABA

Known Issues in newLabel.txt

Line	Issue	Details
4	Missing space in ROIs	844882 should be 844 882 (PMA sub-structure IDs)
103, 138	Duplicate entry	OT (ID=754, Olfactory tubercle) appears twice
115, 120	Duplicate entry	ILM (ID=51, Intralaminar nuclei) appears twice
119, 114	Duplicate entry	MTN (ID=571, Midline group) appears twice
114	Category mismatch	PVT (Paraventricular thalamus) is listed near hypothalamus entries but is anatomically a thalamic structure

The duplicates do not cause errors in doAllROIextract.m (only the primary ID column is matched, not ROIname), but they result in the later duplicate overwriting the earlier entry when type=2 is used.

Brain Region Categories

The label file defines 194 rows (with some duplicates) organized into the following categories:

Isocortex (54 regions)

Abbreviation	Full Name	ABA ID
FP	Frontal pole	184
SomatoMA	Somatomotor areas	500
PMA	Primary motor area	985
SMA	Secondary motor area	993
SomatoSA	Somatosensory area	453
PSSA	Primary somatosensory area	322
PSSA_barrel	Primary somatosensory area, barrel field	329
PSSA_nose	Primary somatosensory area, nose	353
PSSA_lowLimb	Primary somatosensory area, lower limb	337
PSSA_mouth	Primary somatosensory area, mouth	345
PSSA_uplimb	Primary somatosensory area, upper limb	369
PSSA_trunk	Primary somatosensory area, trunk	361
PSSA_unassigned	Primary somatosensory area, unassigned	1231
RLLVA	Rostrolateral lateral visual area	1221
SupplementalSSA	Supplemental somatosensory area	378
GustatoryA	Gustatory area	1057
VisceralA	Visceral area	677
DorsalAA	Dorsal auditory area	1011
LaterolAVA	Laterolateral anterior visual area	1241
PrimaryAA	Primary auditory area	1002
PostAA	Posterior auditory area	1027
VentAA	Ventral auditory area	1018
VisualA	Visual area	669
pVA	Primary visual area	385
alVA	Anterolateral visual area	402
amVA	Anteromedial visual area	394
lVA	Lateral visual area	409
plVA	Posterolateral visual area	425
pmVA	Posteromedial visual area	533
limA	Laterointermediate area	1251
PosthA	Postrhinal area	1261
ACC	Anterior cingulate area	31
dACC	Dorsal anterior cingulate area	39
vACC	Ventral anterior cingulate area	48
prelimbic	Prelimbic area	972
infralimbic	Infralimbic area	44
orbital	Orbital area	714
lateralOA	Lateral orbital area	723
medialOA	Medial orbital area	731
ventralOA	Ventral orbital area	738
AgraInsula	Agranular insular area	95
dRSC	Dorsal retrosplenial area	879
vRSC	Ventral retrosplenial area	886
lAgranularRSC	Lateral agranular retrosplenial area	894
mmAVA	Mediomedial anterior visual area	1281
mmpVA	Mediomedial posterior visual area	1288
medialVA	Medial visual area	1301
PPAC	Posterior parietal association areas	22
AnteriorA	Anterior area	1308
rlVA	Rostrolateral visual area	417
TAA	Temporal association areas	541
PerirhinalA	Perirhinal area	922
EctorhinalA	Ectorhinal area	895

Olfactory Areas (10 regions)

Abbreviation	Full Name	ABA ID
MOB	Main olfactory bulb	507
AOB	Accessory olfactory bulb	151
AON	Anterior olfactory nucleus	159
TT	Taenia tecta	589
DP	Dorsal peduncular area	814
PiriformA	Piriform area	961
NLOT	Nucleus of the lateral olfactory tract	619
COA	Cortical amygdalar area	631
PAA	Piriform-amygdalar area	788
TR	Postpiriform transition area	566

Hippocampal Formation (8 regions)

Abbreviation	Full Name	ABA ID
lEnt	Lateral entorhinal area	918
mEnt	Medial entorhinal area	926
PAR	Parasubiculum	843
POST	Postsubiculum	1037
PRE	Presubiculum	1084
SUB	Subiculum	502
ProS	Prosubiculum	1351
EP	Endopiriform nucleus	942

Amygdala & Striatum (15 regions)

Abbreviation	Full Name	ABA ID
LA	Lateral amygdalar nucleus	131
BLA	Basolateral amygdalar nucleus	295
BMA	Basomedial amygdalar nucleus	319
PA	Posterior amygdalar nucleus	780
CeA	Central amygdala nucleus	536
MeA	Medial amygdalar nucleus	403
Cl	Claustrum	583
CPu	Caudoputamen	672
NAc	Nucleus accumbens	56
LS	Lateral septal nucleus	242
MS	Medial septal nucleus	564
GPe	Globus pallidus, external segment	1022
GPi	Globus pallidus, internal segment	1031
vPAL	Ventral pallidum	835
OT	Olfactory tubercle	754

Hippocampus (4 regions)

Abbreviation	Full Name	ABA ID
CA1	Field CA1	382
CA2	Field CA2	423
CA3	Field CA3	463
DG	Dentate gyrus	726

Thalamus (20 regions)

Abbreviation	Full Name	ABA ID
VAL	Ventral anterior-lateral complex	629
VM	Ventral medial nucleus	685
VP	Ventral posterior complex	709
PP	Peripeduncular nucleus	1044
MG	Medial geniculate complex	475
dLG	Dorsal lateral geniculate complex	170
vLG	Ventral lateral geniculate complex	178
AM	Anteromedial nucleus	127
AD	Anterodorsal nucleus	64
lAM	Interanteromedial nucleus	1120
dAM	Interanterodorsal nucleus	1113
LD	Lateral dorsal nucleus	155
MD	Mediodorsal nucleus	362
STM	Submedial nucleus	366
PVT	Paraventricular thalamus	149
RT	Reticular nucleus	262
LAT	Lateral group of the dorsal thalamus	138
MTN	Midline group	571
ILM	Intralaminar nuclei	51
EPI	Epithalamus	958

Hypothalamus (9 regions)

Abbreviation	Full Name	ABA ID
PVH	Paraventricular hypothalamic nucleus	38
PeriV	Periventricular hypothalamic nucleus	286
DMH	Dorsomedial nucleus	830
AHN	Anterior hypothalamic nucleus	88
MBO	Mammillary body	331
TM	Tuberomammillary nucleus	557
MPN	Medial preoptic nucleus	515
PM	Premammillary nucleus	263
VMH	Ventromedial hypothalamic nucleus	693

Note: PVT (Paraventricular thalamus, ID=149) appears in the label file adjacent to hypothalamus entries but is anatomically a thalamic midline nucleus. In the label file it is listed at line 114 between the thalamus and hypothalamus sections.

Midbrain & Brainstem (21 regions)

Abbreviation	Full Name	ABA ID
DRN	Dorsal raphe nucleus	872
MRN	Median raphe nucleus	679
VTA	Ventral tegmental area	749
MHb	Medial habenula	483
LHb	Lateral habenula	186
SNr	Substantia nigra, reticular part	381
SNc	Substantia nigra, compact part	374
sSC	Sensory-related superior colliculus	302
mSC	Motor-related superior colliculus	298
IC	Inferior colliculus	4
midRN	Midbrain reticular nucleus	128
PAG	Periaqueductal gray	795
PRT	Pretectal region	1100
LR	Linear raphe nucleus	197
NLL	Nucleus of the lateral lemniscus	617
lPB	Lateral parabrachial nucleus	881
mPB	Medial parabrachial nucleus	890
SOC	Superior olivary complex	398
aBST	Anterior bed nuclei of stria terminalis	359
pBST	Posterior bed nuclei of stria terminalis	367
SPF	Subparafascicular nucleus	406

Hindbrain (14 regions)

Abbreviation	Full Name	ABA ID
motP	Motor-related pons	987
CN	Cochlear nuclei	607
DCN	Dorsal column nuclei	720
NTS	Nucleus of the solitary tract	651
SPVC	Caudal spinal nucleus of the trigeminal	429
AMB	Nucleus ambiguus	135
LRN	Lateral reticular nucleus	235
MDRN	Medullary reticular nucleus	395
PGRN	Paragigantocellular reticular nucleus	938
PHY	Perihypoglossal nuclei	154
PPY	Parapyramidal nucleus	1069
VNC	Vestibular nuclei	701
RNMO	Raphe nuclei of medulla oblongata	379

Cerebellum (18 regions)

Abbreviation	Full Name	ABA ID
LING	Lingula (I)	912
CENT2	Lobule II	976
CENT3	Lobule III	984
CUL4	Lobule IV	992
CUL5	Lobule V	1001
CUL4-5	Lobule IV-V	1091
DEC	Declive (VI)	936
FOTU	Folium-tuber vermis (VII)	944
PYR	Pyramus (VIII)	951
UVU	Uvula (IX)	957
NOD	Nodulus (X)	968
SIM	Simple lobule	1007
ANcr1	Crus 1	1056
ANcr2	Crus 2	1064
PRM	Paramedian lobule	1025
COPY	Copula pyramidis	1033
PFL	Paraflocculus	1041
FL	Flocculus	1049

Fiber Tracts & Other Structures (20 regions)

Abbreviation	Full Name	ABA ID
CBX	Cerebellar cortex	1144
CBN	Cerebellar nuclei	519
lotg	Lateral olfactory tract	21
lln	Optic nerve	848
llln	Oculomotor nerve	832
sV	Sensory root of trigeminal nerve	229
Vlln	Facial nerve	798
Vllln	Cochlear nerve	933
cett	Cervicothalamic tract	932
sst	Spinothalamic tract	871
scp	Superior cerebellar peduncle	326
icp	Inferior cerebellar peduncle	1123
corpus-callosum	Corpus callosum	776
cst	Corticospinal tract	784
lfbst	Thalamus-related fibers	896
eps	Extrapyramidal fiber systems	1000
mfbs	Medial forebrain bundle system	991
VS	Ventricular systems	73
grv (1032)	Grooves of the cerebral cortex	1032
grv (1040)	Grooves of the cerebellar cortex	1040

MATLAB Scripts

doAllROIextract.m — Batch ROI Extraction

Extracts multiple ROIs from a normalized atlas volume based on the label definitions.

Inputs:

Parameter	Description
roipath	Path to label file (e.g., newLabel.txt)
datapath	Path to normalized atlas NIfTI file
filename	Output filename for the new atlas
type	Output mode: 1 = preserve original ABA IDs, 2 = assign sequential IDs

Usage:

roipath = 'newLabel.txt';
datapath = 'NormalizedAnno2.nii';
filename = 'newAtlas_roi.nii';

% Type 1: Keep original ABA IDs as voxel values
doAllROIextract(roipath, datapath, filename, 1);

% Type 2: Assign sequential IDs (1, 2, 3, ...) for each region
doAllROIextract(roipath, datapath, filename, 2);

Behavior:

1. Reads the label file as a CSV table using readtable(roipath, 'Delimiter', ',')
2. Loads the normalized annotation NIfTI volume using load_untouch_nii(datapath)
3. For each row in the label file, finds voxels matching the primary ID column value
4. Creates a new volume with either the original IDs (type=1) or sequential row indices (type=2)
5. Saves the resulting atlas as a NIfTI file

Note: The in-code docstring example (roipath = '~/ABA_ROI.nii') is misleading — roipath should point to the text label file, not a NIfTI file. The usage example above is correct.

Note on type=2: When using sequential IDs, the ROI ID assigned is the row number in the label file (1-indexed). If duplicate entries exist in the label file (e.g., OT, ILM, MTN), the later entry overwrites the earlier one.

doOneROIExtract.m — Single ROI Extraction

Extracts a single brain region as a binary mask from an atlas volume.

Inputs:

Parameter	Description
AtlasData	Path to atlas NIfTI file
ROIid	ABA structure ID to extract
filename	Output filename for the binary mask

Usage:

% Extract the paraventricular thalamus (PVT, ID=149) as a binary mask
doOneROIExtract('newAtlas_roi.nii', 149, 'PVT.nii');

% Extract the dorsal raphe nucleus (DRN, ID=872)
doOneROIExtract('newAtlas_roi.nii', 872, 'DRN.nii');

Behavior:

1. Loads the atlas NIfTI file
2. Creates a binary mask where voxels matching ROIid are set to 1
3. Saves the mask as a NIfTI file preserving the original voxel structure

Workflow

                    Allen Brain Atlas
                          │
                          ▼
              ┌──────────────────────┐
              │  Normalization        │
              │  (AllenAtlasNorm.r)  │
              └──────────────────────┘
                          │
                          ▼
              NormalizedAnno2.nii
                          │
                          ▼
              ┌──────────────────────┐
              │  doAllROIextract.m   │◄── newLabel.txt
              │  (batch extraction)   │
              └──────────────────────┘
                          │
                          ▼
              newAtlas_roi.nii
                          │
                          ▼
              ┌──────────────────────┐
              │  doOneROIExtract.m   │
              │  (single ROI mask)    │
              └──────────────────────┘
                          │
                          ▼
              Individual ROI masks
              (e.g., PVT.nii, DRN.nii)
                          │
                          ▼
              ┌──────────────────────┐
              │  fMRI ROI Analysis   │
              │  (extGroupTSROI.m)   │
              └──────────────────────┘

Data Availability

The NIfTI files in this directory (ABA_ROI.nii, atlas.nii, newAtlas_roi.nii, newatlas.nii, NormalizedAnno2.nii, PVT.nii) are not tracked in the git repository due to their size (~11 MB each). The scripts and label files are available in the repository.

To obtain the NIfTI data files, please contact Hiro Taiyo Hamada (hiroaki.hamada@oist.jp).

Relationship to Other Modules

• Input from: Allen Brain Atlas Normalization — provides NormalizedAnno2.nii
• Output to: ROIs — individual ROI masks used for time series extraction
• Used by: Analysis Pipeline — COPE extraction and statistical analysis

References

• Allen Mouse Brain Atlas (CCFv3)
• Allen Brain Atlas API