email: heath.pardoe@nyulangone.org
www: https://sites.google.com/site/hpardoe
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
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
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
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