ABIDE corpus callosum and brain segmentation data

email: heath.pardoe [at] nyumc.org

This page provides data used to investigate changes in corpus callosum area and brain volume in autism spectrum disorders. MRI data from the ABIDE database was used for these analyses [link].

Corpus callosum and brain segmentation images derived from the ABIDE database [zip, 210 Mb]
Corpus callosum area, brain volumes, qualitative scan ratings, and R script [zip, 77k]

A manuscript describing these analyses has been published in the Journal of Autism and Developmental Disorders [link]. If you use the data from this study, please acknowledge our work using the following citation: 

Kucharsky Hiess, R., Alter, R.A., Sojoudi, S., Ardekani, B., Kuzniecky, R., and Pardoe, H.R. (2015) Corpus callosum area and brain volume in autism spectrum disorder: quantitative analysis of structural MRI from the ABIDE database, Journal of Autism and Developmental Disorders, 45(10): 3107-3114, doi: 10.1007/s10803-015-2468-8

How to obtain area/volume measurements from corpus callosum and brain segmentations


Software required: yuki, fsl, itksnap

1. Extract data
unzip abide.cc.bvol.20150121.zip -d my.output.directory


2. View corpus callosum overlaid on midsagittal slice for an individual.
Example command for viewing corpus callosum:
cd my.output.directory
itksnap --compact s --zoom 2 -s ./Yale/0050625/session_1/anat_1/abide_cc.nii ./Yale/0050625/session_1/anat_1/abide_msp.nii

3. Calculate corpus callosum area; note you may need to modify the yuki command for your specific installation.  
cd my.output.directory
for f in `find . -name "abide_cc.nii"`; do echo yuki -W -csv abide.cc.area.csv -cc $f; yuki -W -csv abide.cc.area.csv -cc $f; done

4. Calculate brain volume
for f in `find . -name "*brain_seg.nii.gz"`; do VOL=`fsl5.0-fslstats $f -V | cut -f2 -d" "`; echo $f","$VOL ; echo $f","$VOL >> abide.brain.vol.csv; done
    

How to carry out data analyses using statistics package "R"


1. Run the following command from within R:
> source("source.me.recreate.abide.20150116.R")

2. Type the following commands to obtain useful summary data
 commanddescription 
 summary(quad.fit)Used to assess if corpus callosum is different in autism spectrum disorders. Summary of general linear model with corpus callosum area as dependent variable and diagnosis (asd/control), age, gender, brain volume and site as independent variables.
 summary(quad.fit.subcat)Used to assess if corpus callosum area is different in DSM-IV ASD subcategories. Summary of general linear model with corpus callosum area as dependent variable and DSM-IV category (autism/aspergers/pdd-nos/aspergers-pdd/control), age, gender, brain volume and site as independent variables.
 summary(intracranial.vol.asd)Used to assess if intracranial volume is different in ASD. Summary of general linear model with brain volume as dependent variable and diagnosis (ASD/control), age, gender and site as independent variables
 summary(intracranial.vol.asd.subcat)Used to assess is corpus callosum area is different in DSM-IV ASD subcategories. Summary of general linear model with brain volume as dependent variable and DSM-IV subcategory, age, gender and site as independent variables
 p.val.summarySummary of p-values for similar inferences to quad.fit shown above but for Witelson subregions.



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