UNC Human Brain Atlas Releases

Neonate Hippocampus/Amygdala BCP Multi-Atlas Database v1.0

styner@www.nitrc.org (Martin Styner) — Wed, 23 Mar 2022 14:49:00 GMT

Hippocampus & amgygdala neonate multi-atlas templates, updates the UCI/UNC atlases, only contains templates derived from the Baby Connectome Project, both original presentation and mirrored presentation are used.
Manual segmentation information is in the pdf in the release

Neonate Scan Rescan Database Scan - Rescan Neonate MRI - Tissue & Structural Segmentations

styner@www.nitrc.org (Martin Styner) — Mon, 04 Apr 2016 14:56:00 GMT

Adding the results for the AutoSeg based multi-atlas neonate Hippocampus and amygdala segmentation
6 subjects, healthy/typical subjects, anonymized
- Subjects accumulated from 3 different studies of neonates scanned at Biomedical Image Research Center at the University of North Carolina (UNC), as well as at the University of California, Irvine.
- Scans originated from whole-body 3T Siemens Tim Trio scanners at UNC (4 cases) and UCI (2 cases).
- For these subjects a second set of T1weighted and T2weighted scans were acquired in the same scanning session, as the first set was considered of borderline quality by the scanning technicians. In all these cases, subsequent quality control procedures by trained image analysis experts showed all scans to pass quality assessment for structural morphometric analysis.
- This small size neonate scan-rescan database captures the low signal-to- noise and presence of motion very common in early postnatal scans and thus is well suited to estimate reliability of image processing procedures.
- As at least 50% of these images were assessed to be of borderline quality by the scanner personnel, this scan-rescan database is likely to overestimate the expected variability as compared to the average setting.

Neonate Hippocampus Amygdala Multi-Atlas Database Neonate Hippocampus/Amygdala Multi-Atlas Database

styner@www.nitrc.org (Martin Styner) — Tue, 06 Oct 2015 17:11:00 GMT

1st release of multi-atlas neonate hippocampus & amygdala segmentation atlas/database:
- All subjects anonymized and skull stripped
- All subjects scanned within the first 5 weeks post-natally
- All subjects scanned at UC Irvine on a whole-body 3T Siemens Tim Trio scanner

Any publications making use of this database needs to acknowledge the following NIH grants MH091351, MH091645, HD079124

UNC_Neonate_MultiSubject_Atlas UNC_Neonate_MultiSubject_Atlas_8cases_flipped

fbudin@www.nitrc.org (Francois Budin) — Wed, 28 Jan 2015 14:12:00 GMT

This atlas is composed of 8 neonate subjects. Each subject folder contains a T1w image, a T2w image, and a tissue segmentation (white matter, gray matter, CSF). Each case has also been flipped.

UNC_Adult_Brain_Atlas UNC_Adult_Brain_Atlas_2

cvachet@www.nitrc.org (Clement Vachet) — Thu, 16 Jun 2011 15:05:00 GMT

[b]Authors: [/b]Clement Vachet, Clementine Ouziel, Elizabeth Bullitt, Brad Davis, Guido Gerig, Martin Styner
[b]Description:[/b]
This atlas has been created using 50+ healthy adult cases (between 20 and 59 years old) plus inverted ones. Not only is the T1-weighted image provided (with and without skull), but also tissue segmentation probability maps (white matter, gray matter, CSF, rest) and a 27-lobe parcellation map.
[b]Sponsor:[/b] This work is funded in part by the National Alliance for Medical Image Computing (NAMIC), a NIH Roadmap for Medical Research, Grant U54 EB005149, and by UNC Neurodevelopmental Disorders Research Center HD 03110.
[b]Institution:[/b] University of North Carolina at Chapel Hill

UNC_Pediatric_Brain_Atlas UNC-MNI_Pediatric_1year_Brain_Atlas

cvachet@www.nitrc.org (Clement Vachet) — Wed, 19 Oct 2011 15:30:00 GMT

We provide a symmetric, unbiased, 1-year-old T1-weigthed atlas template computed via joint deformable registration that simultaneously minimizes the differences of intensity and transformation from 104 training images from a 1-year-old dataset within the Autism IBIS study (controls and children at high familial risk of autism) (Fonov et al. 2011).
Not only is the T1-weighted image provided (with and without skull), but also tissue segmentation probability maps optimized for ABC (Atlas Based Classification software), a 26-lobe parcellation map, and a subcortical structures label map (including amygdala, caudate, hippocampus, pallidus, putamen).
Atlas orientation: RAI

Package information:
- BrainsegAtlas/:
    - pediatric-atlas-1year-sym-T1-IGM-RAI_06_2011/: T1-weighted atlas with tissue priors
    - pediatric-atlas-1year-sym-stripped-T1-IGM-RAI_06_2011/: skull-stripped T1-weighted atlas with tissue priors
- BrainROIAtlas/:
    - pediatric-atlas-1year-sym-T1-IGM-RAI_06_2011/: skull-stripped T1-weighted atlas with 26-lobe parcellation map, cerebellum-brainstem-cerebrum parcellation map, subcortical structures label map, enlarged masks around lateral ventricles.

Contribution:
- IBIS Network for the training dataset
- Montreal Neurological Institute (McGill University) for the generation of T1-weighted atlas
Reference: Fonov, V., Evans, A.C., Botteron, K., Almli, C.R., McKinstry, R.C., Collins, D.L., 2011.Unbiased average age-appropriate atlases for pediatric studies.Neuroimage 54, 313-327.
- UNC-Chapel Hill for the generation of tissue priors and parcellation maps

Acknowledgement:
This pediatric atlas has been made available by UNC Chapel Hill, Montreal Neurological Institute, and the IBIS Network.

UNC_Pediatric_Brain_Atlas UNC_Pediatric_Brain_Atlas_2

cvachet@www.nitrc.org (Clement Vachet) — Thu, 16 Jun 2011 18:00:00 GMT

[b]Authors:[/b] Martin Styner, Clement Vachet, Eric Harmon, Rachel Gimpel Smith, Cedric Mathieu, Guido Gerig, Brad Davis, Sarang Joshi, Joe Piven, Heather Cody Hazlett
[b]Description:[/b]
This symmetric atlas has been created using 10 4-year old cases plus inverted ones. Not only is the T1-weighted image provided (with and without skull), but also tissue segmentation probability maps (white matter, gray matter, CSF, rest), subcortical structures probability maps (amygdala, caudate, hippocampus, pallidus, putamen), and a 25-lobe parcellation map.
[b]Sponsor:[/b] NAMIC: National Alliance for Medical Image Computing [b][/b]
[b]Institution:[/b] University of North Carolina at Chapel Hill

Orientation: RAI

UNC_Pediatric_Brain_Atlas UNC_Pediatric_Brain_Atlas_1

cvachet@www.nitrc.org (Clement Vachet) — Mon, 26 Oct 2009 20:41:00 GMT

[b]Authors:[/b] Martin Styner, Clement Vachet, Eric Harmon, Rachel Gimpel Smith, Cedric Mathieu, Guido Gerig, Brad Davis, Sarang Joshi, Joe Piven, Heather Cody Hazlett

[b]Description:[/b]
This symmetric atlas has been created using 10 4-year old cases plus inverted ones. Not only is the T1-weighted image provided (with and without skull), but also tissue segmentation probability maps (white matter, gray matter, CSF, rest), subcortical structures probability maps (amygdala, caudate, hippocampus, pallidus, putamen), and a 25-lobe parcellation map.

[b]Sponsor:[/b] NAMIC: National Alliance for Medical Image Computing

[b]Institution:[/b] University of North Carolina at Chapel Hill

Orientation: RAI

UNC_Adult_Brain_Atlas UNC_Adult_Brain_Atlas_1

cvachet@www.nitrc.org (Clement Vachet) — Mon, 26 Oct 2009 20:43:00 GMT

[b]Authors: [/b]Clement Vachet, Elizabeth Bullitt, Brad Davis, Guido Gerig, Martin Styner

[b]Description:[/b]
This atlas has been created using 50+ healthy adult cases (between 20 and 59 years old) plus inverted ones. Not only is the T1-weighted image provided (with and without skull), but also tissue segmentation probability maps (white matter, gray matter, CSF, rest) and a 27-lobe parcellation map.

[b]Sponsor:[/b] This work is funded in part by the National Alliance for Medical Image Computing (NAMIC), a NIH Roadmap for Medical Research, Grant U54 EB005149, and by UNC Neurodevelopmental Disorders Research Center HD 03110.

[b]Institution:[/b] University of North Carolina at Chapel Hill

UNC_Elderly_Brain_Atlas UNC_Elderly_Brain_Atlas_1

cvachet@www.nitrc.org (Clement Vachet) — Mon, 26 Oct 2009 20:44:00 GMT

[b]Authors:[/b] Clement Vachet, Elizabeth Bullit, Laurence Katz, Bonita Marks, Bradley Davis, Martin Styner
[b]Description:[/b] This atlas has been created using 26 healthy elderly cases (60+ years old). Not only is the T1-weighted image provided, but also subcortical structures probability maps (amygdala, caudate, hippocampus, pallidus, putamen), and a 26-lobe parcellation map.
[b]Sponsor:[/b] This work is funded in part by:
- the National Alliance for Medical Image Computing (NAMIC), a NIH Roadmap for Medical Research, Grant U54 EB005149
- UNC Neurodevelopmental Disorders Research Center HD 03110.
- UNC's Biomedical Research Imaging Center seed grant (PI Dr. Bonita L.Marks, "Role of Recreational Sport Participation on Cerebral White Matter Integrity in Older Adults") and A&S Interdisciplinary Initiative Grant
- UNC Casilab's grant NIH-NIBIB R01-EB000219

Some of the MR brain images from healthy volunteers used to create this atlas were collected and made available by the CASILab (led by Dr. Elizabeth Bullitt) at The University of North Carolina at Chapel Hill.

[b]Institution:[/b] UNC Chapel Hill - Neuro Image Research and Analysis Laboratories