deletions | additions       diff --git a/sectionAim_2__subsec.tex b/sectionAim_2__subsec.tex  index 5463448..9782349 100644  --- a/sectionAim_2__subsec.tex  +++ b/sectionAim_2__subsec.tex 
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Resting state fMRI(3mm isotropic voxel size, TR = 2.1s, TE = 27ms, 27 slices interleaved, 240 volumes) and MPRAGE(Sagittal, 1mm isotropic voxel size, TR=2.3s, TE=2.98ms, TI=900ms) scans were acquired from 250 patients (aged 26-74, mean age = 50) diagnosed with MS from the UCSF EPIC study. The high and low disability groups will be selected from this set of patients. The upper motor disability of MS patients was evaluated by the nine-hole-peg-test (NHPT) \cite{fischer1999multiple}. Briefly, the patients were asked to place nine pegs in a grid of 9 holes, one at a time using 1 hand, and then remove the pegs one at a time, all while being timed. Both hands were evaluated twice and the times were averaged and z-scored against healthy controls.   \subsubsection*{Data Preprocessing}  FreeSurfer[5] FreeSurfer  version 5.3 will be run on MPRAGE structural scans of the healthy controls and MS patients. Careful editing of the the pial and white matter surfaces will ensure proper affine registration of the resting state scan to the structural surface. Resting state preprocessing steps include the following: simultaneous slice timing and motion correction [6], correction,  artifact detection, nuisance filtering of motion parameters, artifacts, anatomical and temporal CompCor[2] CompCor  from the fMRI timeseries, bandpass filtering(0.01-0.1 Hz), isotropic volume smoothing (6mm), cortical surface smoothing(10mm), mapping the timeseries to the fsaverage5 surface via FreeSurfer, and finally normalization to MNI space via ANTS[1]. ANTS.