open-discussion > Schiz_Bull_2008 Segmentation Data Release
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Jul 25, 2011  03:07 PM | David Kennedy
Schiz_Bull_2008 Segmentation Data Release
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:

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

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'.

Jul 25, 2011  08:07 PM | David Kennedy
RE: Schiz_Bull_2008 Segmentation Data Release
So, we're now in the 'promotion' phase of this first release.  I've posted an announcement regarding the availablity of this data to: NIDAG, SPM, FSL, INCH Datasharing Task Force and INCF datasharing Workshop groups.

Can YOU think of other places to promote this?  If so, fees free to advertise for us, or at least let us know where you suggest, and we'll try and follow up.

A 'news item' or somesort of other publication is in the works, tho that's a more lugubrious dissemination mode...  I hope the News release from this on NITRC will make NITRC's home page soon, that'll hit Facebook and Twitter, now that'd realtime social networking dissemination!

(I wish this editor had spel checking..., sounds like a eature request for NITRC)