divyanganar

% to organise my data and get the same variables from it

% lh_thickness_VarNames = all_data.Properties.VariableNames(82:115);
% rh_thickness_VarNames = all_data.Properties.VariableNames(119:152);
% lh_volume_VarNames = all_data.Properties.VariableNames(156:189);
% rh_volume_VarNames = all_data.Properties.VariableNames(192:225);
% lh_subcortical_VarNames = all_data.Properties.VariableNames([232,233,234,235,239,240,242]);
% rh_subcortical_VarNames = all_data.Properties.VariableNames([250,251,252,253,254,255,256]);
% lh_area_VarNames = all_data.Properties.VariableNames(8:41);
% rh_area_VarNames = all_data.Properties.VariableNames(45:78);

divyanganar

path = '/data/nimble/work/Divyangana_Rakesh/resting_state/t3/fmriprep';

subjectNames = dir(sprintf('%s',path));
subs = startsWith({subjectNames.name},'sub') & ~contains({subjectNames.name},'.html');
subject_names = {subjectNames.name};
subject_names = subject_names(subs);

TR = 1.4;

divyanganar

path = '/data/nimble/work/Divyangana_Rakesh/resting_state/t3/fmriprep';

subjectNames = dir(sprintf('%s',path));
subs = startsWith({subjectNames.name},'sub') & ~contains({subjectNames.name},'.html');
subject_names = {subjectNames.name};
subject_names = subject_names(subs);

TR = 1.4;

upper=((1/TR)/2)*100; upper=num2str(upper);

divyanganar

 function [mat, fwd_percent] = fwd(subj_numb, filename, exit_file, csv_file, run)
        mat = textread(filename);
        radius = 50; %mm
        ts = mat;
        temp = mat(:,4:6)*180/pi; %convert to degrees
        temp = (2*radius*pi/360)*temp;
        ts(:,4:6) = temp;
        dts = diff(ts);
        fwd = sum(abs(dts),2);
        a = 0.0;

divyanganar

Things that need to be done before the workshop:

1. Please ensure that you have a laptop with a 64 bit OS for the workshop
2. If you haven't had your imaging lab induction: please ask Chester to create an account for you on at least one of the imaging computers (for remote access). You don't need to do the induction with him yet, this is just to ensure that you can remotely access and copy some files.
3. Please open an account with spartan (https://dashboard.hpc.unimelb.edu.au/getting_started/). Best to do this today because it can take a couple of days for the request to get approved.
4. Install docker and run the command per the instructions below

Instructions for Docker

divyanganar

%% make a cell array of all subject names
% defines the path for the data, extracts the directory names
path = '/Users/Divyangana/Desktop/orwa/orwa_rest/'; 
subs = dir(path); 

 % creates a boolean array for all directories that start with 1 (which is our subject ids)
index_for_directories = startsWith({subs.name},'1');

% creates a cell array of all directories in the path (subject ids + other folders)

divyanganar

#!/bin/bash

echo "starting to convert files from old to bids format..."

i=0

for sub_path in ./old/*; do

        let "i+=1"
        printf -v index "%02d" $i