This repository offers tools for performing a subcortical volume quantification on brain Magnetic Resonance Imaging (MRI) imaging data. The purpose of these tools is to do a volumetric quantification of subcortical brain structures to study the potential effects of the chemo-brain in patients with breast cancer.
It contains two scripts:
- 'Subcortical_Volumes_normalized.sh': An FSL - compreensive MRI analysis tools from FMRIB Software Library, version 5.0.10 (1) - bash script that uses FSLstats to quantify the volumes of 15 subcortical brain structures (bilateral nucleus accumbens, amygdala, caudate, hippocampus, globus pallidum, putamen, and thalamus, and brainstem)
- 'Subcortical_volumes_comparison.R': An R script to compare the normalized subcortical volumes of healthy controls (HC) and breast cancer patients (BC) determined in the first step, using unpaired and paired t-tests, respectively, between HC vs BC at baseline (M0) and BC at M0 vs BC at 6 months after treatment (M6).
For running the subcortical quantification, the following must be provided on your main directory:
- A folder with your FSL SIENAX results (Total brain volume and V-scaling factor estimates).
- A folder with your FSL FIRST results ('T1_first_all_fast_firstseg.nii.gz' files with the segmentation output).
In order to run the bash script type these commmands on the command line:
$ cd path_to_script
$ chmod a+x Subcortical_Volumes_normalized.sh
$ ./Subcortical_Volumes_normalized.sh
Our work is based on the following FSL tools: (1) M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009
If you use any of these in your research, please don't forget to acknowledge our work. This repository was created by Ana Sofia Castro Verde. For questions, please contact ana.castroverde@research.fchampalimaud.org.