CANDI Neuroimaging Access Point News

New CANDI-supported paper: Data Citation in Neuroimaging

David Kennedy — Mon, 13 Feb 2017 3:01:57 GMT

Data sharing and reuse, while widely accepted as good ideas, have been slow to catch on in any concrete and consistent way. One major hurdle within the scientific community has been the lack of widely accepted standards for citing that data, making it difficult to track usage and measure impact. Within the neuroimaging community, there is a need for a way to not only clearly identify and cite datasets, but also to derive new aggregate sets from multiple sources while clearly maintaining lines of attribution. This work presents a functional prototype of a system to integrate Digital Object Identifiers (DOI) and a standardized metadata schema into a XNAT-based repository workflow, allowing for identification of data at both the project and image level. These item and source level identifiers allow any newly defined combination of images, from any number of projects, to be tagged with a new group-level DOI that automatically inherits the individual attributes and provenance information of its constituent parts. This system enables the tracking of data reuse down to the level of individual images. The implementation of this type of data identification system would impact researchers and data creators, data hosting facilities, and data publishers, but the benefit of having widely accepted standards for data identification and attribution would go far toward making data citation practical and advantageous.

See https://www.ncbi.nlm.nih.gov/pubmed/27570508 for more details.

SchizBull 2008 Outlines Released

David Kennedy — Fri, 09 Nov 2012 4:12:34 GMT

We are pleased to announce the release of the original 'outline' files for the SchixBull-2008 (Frazier JA, Hodge SM, Breeze JL, Giuliano AJ, Terry JE, Moore CM, Kennedy DN, Lopez-Larson MP, Caviness VS, Seidman LJ, Zablotsky B, Makris N. Diagnostic and sex effects on limbic volumes in early-onset bipolar disorder and schizophrenia. Schizophr Bull. 2008 Jan;34(1):37-46.) project. This release can be accessed at http://www.nitrc.org/frs/download.php/5049/SchizBull_2008_otl_V1.0.tar.gz

While the segmentation results have long been available in the NIfTI n-ary format, this release contains the original outline files (.otl) as generated in the Cardviews software. As the intrinsic data model for the 'outline' of Cardviews versus the 'voxel-label' based NIfTI differ, there are minor voxel differences in these two versions relative to the exact intent and execution of the segmentation as processed by the original segmenter. While the NIfTI versions of the segmentation are deemed to be more accessible for reuse by the community, the release of the .otl versions are provided for completeness and transparancy.

Schizophrenia Bulletin 2008 Data Released on NITRC-IR

Christian Haselgrove — Thu, 28 Jun 2012 1:58:27 GMT

The Schizophrenia Bulletin 2008 data is now available for download on NITRC-IR. Structural data and manual segmentations are avaialable, and data can be filtered by basic demographics before download. Segmentation preview thumbnails are also available as you browse.

See the cs_schizbull2008 project at NITRC-IR: http://nitrc.org/ir/.

SchizBull_2008 version 1.2 released

David Kennedy — Thu, 01 Mar 2012 2:05:47 GMT

We are pleased to announce the release of version V1.2 of the Schizophrenia Bulletin 2008 data. With this release, there is one minor 'bug' fix, and the linear and non-linear registrations for all subjects to the MNI152 space are provided. See release notes at http://www.nitrc.org/frs/shownotes.php?release_id=1880 for complete details.

CANDIShare Atlases updated to V1.1

David Kennedy — Tue, 14 Feb 2012 7:34:27 GMT

We are pleased to announce the next release of the CANDIShare atlases. Version 1.1 of the CANDIShare Atlases includes Linear and nonlinear registration to the NMI152_T1_2mm space (FLIRT & FNIRT). Also includes structural label probabilities, as well as maximum probability labeling templates, and group averaged MRI scans for the diagnostic groups reported in Frazier JA, Hodge SM, Breeze JL, Giuliano AJ, Terry JE, Moore CM, Kennedy DN,
Lopez-Larson MP, Caviness VS, Seidman LJ, Zablotsky B, Makris N. Diagnostic and sex effects on limbic volumes in early-onset bipolar disorder and schizophrenia. Schizophr Bull. 2008 Jan;34(1):37-46.

CANDIShare Atlases V1.0 Released

David Kennedy — Tue, 20 Dec 2011 1:26:46 GMT

Introducing CANDIShare Schiz_Bull_2008 Atlases Version 1.0. This is the initial set of atlases generated from the image and segmentation results in the CANDIShare release.

The atlases are based upon MRI images and segmentation results of all 4 diagnostic groups (Healthy Controls (N=29), Schizophrenia Spectrum (N=20), Bipolar Disorder with Psychosis (N=19), and Bipolar Disorder without Psychosis (N=35)) from the article: Frazier JA, Hodge SM, Breeze JL, Giuliano AJ, Terry JE, Moore CM, Kennedy DN, Lopez-Larson MP, Caviness VS, Seidman LJ, Zablotsky B, Makris N. Diagnostic and sex effects on limbic volumes in early-onset bipolar disorder and schizophrenia. Schizophr Bull. 2008 Jan;34(1):37-46.

This version of the atlases are based upon afine registration to the MNI152_2mm space.

Check out: http://www.nitrc.org/frs/download.php/4189/Atlases_V1.0.tar.gz
Enjoy!

ACNP 2011 Poster

David Kennedy — Tue, 06 Dec 2011 7:46:36 GMT

Is now available in the Docs tab. Poster will be presented in the Wednesday, Dec 7, 2011 poster session. Stop by if you're in the neighborhood.

Segmentation Data Public Release

David Kennedy — Fri, 29 Jul 2011 7:52:31 GMT

Introducing CANDIShare Schiz_Bull_2008 Version 1.1. With this release we have added the CMA 'general' segmentation for all 103 subjects in the prior Schiz_Bull_2008 V1.0 release.

Get it now at: http://www.nitrc.org/projects/candi_share/

We include the preprocessed MRI images and CMA 'general' segmentation results of all 4 diagnostic groups (Healthy Controls (N=29), Schizophrenia Spectrum (N=20), Bipolar Disorder with Psychosis (N=19), and Bipolar Disorder without Psychosis (N=35)) from the article: Frazier JA, Hodge SM, Breeze JL, Giuliano AJ, Terry JE, Moore CM, Kennedy DN, Lopez-Larson MP, Caviness VS, Seidman LJ, Zablotsky B, Makris N. Diagnostic and sex effects on limbic volumes in early-onset bipolar disorder and schizophrenia. Schizophr Bull. 2008 Jan;34(1):37-46.

The release contains 4 files, one for each diagnostic group, provided as a gziped tar file of a set of directories containing the data.

The root directory is for the paper, SchizBull_2008/, and contains subdirectories for the 4 diagnostic groups: Healthy Controls (HC), bipolar disorder without psychosis (BPDwithoutPsy), bipolar disorder with psychosis (BPDwithPsy) and schizophrenia spectrum (SS). Each of these subdirectories will contain separate subdirectories for each subject. These subject directories contain the CMA preprocessed image that was submitted to the anatomic segmentation process, and the results of the general segmentation. These files are of type NIfTI (nii.gz) and called {$SUBJECT_ID}_{$TYPE}.nii.gz; where $TYPE is 'procimg' for preprocessed images, and 'seg' for general segmentation. The seg results are 'n-ary' images, where the fill value represents the specific anatomic region.

Each of the diagnostic group tar files will 'unpack' onto the same directory structure and fill in the released subset of data.

The nature of the CMA preprocessing includes positional normalization to put the image into the standard orientation of the Talairach coordinate space, and bias field correction as described in: Worth AJ, Makris N, Patti MR, Goodman JM, Hoge EA, Caviness VS Jr, Kennedy DN. Precise segmentation of the lateral ventricles and caudate nucleus in MR brain images using anatomically driven histograms. IEEE Trans Med Imaging. 1998 Apr;17(2):303-10.

The basic segmentation procedures followed by the CMA are overviewed in: Filipek PA, Richelme C, Kennedy DN, Caviness VS Jr., The young adult human brain: an MRI-based morphometric analysis. Cereb Cortex. 1994 Jul-Aug;4(4):344-60.

Diagnostic group basic demographic information is provided in the diagnostic subdirectory in a .csv file entitled {$DIAG}_Basic_Demographics.csv. This file contains age, gender, and handedness for each of the subjects in the diagnostic group.

The fill value codes for the 'seg' files can be found in the 'seg_fill_values.txt' file to be found in the Documents section of the CANDIShare NITRC project. The fill values are correct for automatic interpretation using the 'CMA Subcortical' color pallet in fslview and the Freesurfer 'FreeSurferColorLUT.txt'.

Enjoy!

CANDIShare Fourth Data Release

David Kennedy — Tue, 27 Jul 2010 11:24:59 GMT

We are happy to announce the release of the CMA preprocessed images of the Schizophrenia Spectrum subjects group (N=20) from the article: Frazier JA, Hodge SM, Breeze JL, Giuliano AJ, Terry JE, Moore CM, Kennedy DN, Lopez-Larson MP, Caviness VS, Seidman LJ, Zablotsky B, Makris N. Diagnostic and sex effects on limbic volumes in early-onset bipolar disorder and schizophrenia. Schizophr Bull. 2008 Jan;34(1):37-46. (see http://www.nitrc.org/docman/view.php/377/791/Schizophrenia%20bulletin%202008%20Frazier.pdf)

The data release is located at: http://www.nitrc.org/frs/download.php/2340/SchizBull_2008_SS_Procimg.tar.gz
See release notes at: http://www.nitrc.org/frs/shownotes.php?release_id=1133

Subsequent releases over the next few months will comprise the 'general segmentation' and 'cortical parcellation' for each.

Stay tuned, register as a 'User' of the this project and join the discussion!

CANDIShare Third Data Release

David Kennedy — Tue, 27 Jul 2010 6:08:57 GMT

We are happy to announce the release of the CMA preprocessed images of the Bipolar Disorder with Psychosis subjects group (N=19) from the article: Frazier JA, Hodge SM, Breeze JL, Giuliano AJ, Terry JE, Moore CM, Kennedy DN, Lopez-Larson MP, Caviness VS, Seidman LJ, Zablotsky B, Makris N. Diagnostic and sex effects on limbic volumes in early-onset bipolar disorder and schizophrenia. Schizophr Bull. 2008 Jan;34(1):37-46. (see http://www.nitrc.org/docman/view.php/377/791/Schizophrenia%20bulletin%202008%20Frazier.pdf)

The data release is located at: http://www.nitrc.org/frs/download.php/2338/SchizBull_2008_BPDwPsy_procimg.tar.gz
See release notes at: http://www.nitrc.org/frs/shownotes.php?release_id=1132

Subsequent releases over the next few months will comprise the remaining diagnostic group (schizophrenia spectrum (SS)) as well as the 'general segmentation' and 'cortical parcellation' for each.

Stay tuned & Join the discussion!