vsoch/confirmation_email.m

## confirmation_email.m
function confirmation_email(contactemail)

% CONFIRMATION_EMAIL
% Vanessa Sochat
%
% This script sends confirmation emails for imaging and battery appointments
% added to the calendar the previous day.
%
% -------------------------------------------------------------------------
% VARIABLES:
%
% contactemail: An email address that you want to be notified in
% the case of error
%
% -------------------------------------------------------------------------
% DEPENDENCY:
% For the script to work, it must have access to each of the appointment
% private calendars (URL's hard coded), and the data in the calendar must
% have the user email as the first thing in the Description field, like so
%
% Name: Jane Doe
% Phone: (999) 999-9999
% E-mail: jane.doe@duke.edu
%
% poozie.mat must be in the same folder it is running from
%
% schedule.csv: Downloaded by the batch script just before running
% the matlab script - this file contains all subject specific info that is
% used to look up an individual based on name.
%--------------------------------------------------------------------------
% OUTPUT:
% A log of confirmation email info is saved, and all files are located
% under:
%
% Y:/Scripts/Appointments
% -------------------------------------------------------------------------

%--------------------------------------------------------------------------
% Set up mail credentials
%--------------------------------------------------------------------------

load poozie.mat
email_count=0;

% Path to the reminder and directions sheet
reminder_directions = 'Y:/Scripts/Appointments/Reminder_and_Directions.pdf';
% Then this code will set up the preferences properly:
setpref('Internet','E_mail',poozie);
setpref('Internet','SMTP_Server','smtp.gmail.com');
setpref('Internet','SMTP_Username',poozie);
setpref('Internet','SMTP_Password',pooziepa);
props = java.lang.System.getProperties;
props.setProperty('mail.smtp.auth','true');
props.setProperty('mail.smtp.socketFactory.class', 'javax.net.ssl.SSLSocketFactory');
props.setProperty('mail.smtp.socketFactory.port','465');


%--------------------------------------------------------------------------
% Read in appointment file (schedule.csv) downloaded from server
%--------------------------------------------------------------------------

% If the file exists, read it in.  If it doesn't, exit with an error,
% record error to the log, and email Vanessa about error.

if exist('schedule.csv','file')
    fid = fopen('schedule.csv');
else
    % Initialize and print to file
    fid = fopen('ERROR_LOG.txt', 'a');
    fprintf(fid, 'Date: ');
    fprintf(fid,'%s\n', date');
    fprintf(fid, 'Schedule file does not exist! Check download.');
    fclose(fid);
    % If the user has provided an email, alert that email of the failure:
    if exist('contactemail','var')
        sendmail(contactemail,'Message from Rem_Email.m',[  'The script exited with error on ' date ' while sending out ' days ' day reminders for the ' calendar ' calendar. '],'');
    end
        error('Schedule file does not exist');
end

% READ APPOINTMENT INFORMATION FROM FILE

% First read in the header fields
H = textscan(fid, '%s %s %s %s %s %s %s %s %s %s %s \n', 'delimiter', ',');
% StartTime {H1}
% EndTime (H2)
% First Name (H3)
% Last Name (H4)
% Phone (H5)
% Email (H6)
% Type (H7)
% Calendar (H8)
% Duke Unique ID (H9)
% Text Message? (H10)
% Phone Carrier (H11)

% Then read the data from the rest of the file
C = textscan(fid, '%s %s %s %s %s %s %s %s %s %s %s %s %s', 'delimiter', ',');

% StartDate {C1}
% StartTime (C2)
% EndDate (C3)
% EndTime (C4)
% First Name (C5)
% Last Name (C6)
% Phone (C7)
% Email (C8)
% Appointment Type (C9)
% Clinician (C10)
% Unique ID (C11)
% Text Message? (C12)
% Phone Carrier (C13)

% Now we convert a cell array into an array of strings so we can read each
% one, only for the fields that we are interested in.
FirstNames = C{5};
LastNames = C{6};
Phones = C{7};
Emails = C{8};
Txt = C{12};
Carriers = C{13};

fclose(fid);
clear C H fid;

%--------------------------------------------------------------------------
% Download latest appointments from imaging and computer calendar to file
%--------------------------------------------------------------------------

% CD to directory for saving current appointment files
cd('Y:/Scripts/Appointments/');

% Download and save the calendar data, if it doesn't already exist in the
% folder (since the reminder emails are sent just before and haven't been
% deleted by the batch script, these files should already exist!)

if exist('imaging.txt','file')==0
    calie{1} = urlwrite(schmoogie,'imaging.txt','get',{});
else
    calie{1} = 'imaging.txt';
end
meetingloc{1} = 'Soc-Psych 07';
cal{1} = 'Imaging';

if exist('computer.txt','file')==0
    calie{2} = urlwrite(yebya,'computer.txt','get',{});
else
    calie{2} = 'computer.txt';
end
meetingloc{2} = 'LSRC B Lobby';
cal{2} = 'Computer';

%--------------------------------------------------------------------------
% Read appointments from the file and save to variable
%--------------------------------------------------------------------------

% Open the subject appointment file, which was an .ical file that we open as
% a text file

for v=1:2

fln = fopen(calie{v});

% Create a subject count variable
appt_count=0;

% Set the current appointment date to today, so we can stop reading the
% file when the appointments go into the past.
Appointment=date;

% Set today's date in a number format for easy comparison
today = datenum(date);

while ~feof(fln)

        % We need to make sure that we only read in appointments for today and
        % in the future, so we do a comparison between the current appointment
        % that is being read.  We use a do-->while loop so that the comparison
        % until after a subject has been

        % Read in line
        currentline = fgetl(fln);

        % Look to see if we have a date line, which starts with 'DSTART'
        if regexp(currentline, 'DTSTART', 'once');
            %if yes, pull the date and time from this line, and format
            year = currentline(9:12);
            month = currentline(13:14);
            day = currentline(15:16);
            appointment = datestr([ year ' ' month ' ' day ]);
            time = currentline(18:21);
            time = str2double(time);

            % The time is 4 hours in the future, so we subtract 4:
            time = time - 400;

            % Convert military time to standard time
            if (time > 1259)
                time = time-1200;
                period = 'pm';
            else
                if (time >= 1200) && (time <= 1259)
                    period = 'pm';
                else
                    period = 'am';
                end
            end

            % Format time with a ":" by separating the last two characters
            % from the first, and sticking them together with a ":"
            time = num2str(time);
            time_end = time(length(time)-1:length(time));
            time_beg = regexprep(time, time_end, '','once');

            % Put it all together into a user friendly format for printing
            time = [ time_beg ':' time_end ' ' period ];

            % If the appointment is from before today, we don't want to do
            % anything.
            if(today > datenum(appointment))

            else
                %Add another subject to the array if they aren't from the past
                appt_count = appt_count +1;
                APPTS(appt_count)= struct('First','','Last','','Email', '','Phone','','Appointment', appointment, 'Time', time,'Text','','Carrier','','Created','');
            end
        end

        % Look to see if we have a date created line, which starts with 'CREATED'
        if regexp(currentline, 'CREATED', 'once');
            %if yes, pull the date and time from this line, and format
            create_year = currentline(9:12);
            create_month = currentline(13:14);
            create_day = currentline(15:16);
            created = datestr([ create_year ' ' create_month ' ' create_day ]);

            % If the appointment is from before today, we don't want to do
            % anything.
            if(today > datenum(appointment))

            else
                APPTS(appt_count).Created = created;
            end
        end

        % Look to see if we have a participant info line:
        if regexp(currentline, 'DESCRIPTION', 'once');
            % Only read the line if there is data there, meaning the length
            % is greater than 12 (the length of DESCRIPTION:)
            if length(currentline) > 12
                % If the appointment is from the past, skip it, as we did
                % above
                if (today > datenum(appointment))

                else
                    %if yes, first get rid of the 'DESCRIPTION:Name: ' section
                    currentline = regexprep(currentline, currentline(1:18), '','once');
                    % Put the first name into a variable by finding the end of it,
                    % marked by a space
                    marker = regexp(currentline, ' ', 'once');
                    name = currentline(1:marker-1);
                    currentline = regexprep(currentline, currentline(1:marker), '','once');
                    % Put the last name into a variable by finding the end,
                    % marked by a space
                    marker = regexp(currentline, ' ', 'once');
                    lastname = currentline(1:marker-1);
                    % Add name to the data structure
                    APPTS(appt_count).First = deblank(name);
                    APPTS(appt_count).Last = deblank(lastname);

                end
            end
        end
        % Take in the name from the summary field, in case we need it
        if regexp(currentline, 'SUMMARY', 'once');
            currentline = regexprep(currentline, currentline(1:8), '','once');
            % Put the first name into a variable by finding the end of it,
            % marked by a space
            marker = regexp(currentline, ' ', 'once');
            name = currentline(1:marker-1);
            currentline = regexprep(currentline, currentline(1:marker), '','once');
            % Put the last name into a variable by finding the end,
            % marked by a space
            marker = regexp(currentline, ' ', 'once');
                if isempty(marker)
                    lastname = currentline;
                else
                    lastname = currentline(1:marker-1);
                end

                % In the case that the name was not present in the
                % DESCRIPTION, we can get it from the Summary!
                if isempty(APPTS(appt_count).First)
                    APPTS(appt_count).First = deblank(name);
                end
                if isempty(APPTS(appt_count).Last)
                    APPTS(appt_count).Last = deblank(lastname);
                end
        end
end

%--------------------------------------------------------------------------
% Find rest of subject info by reading from Appointment file
%--------------------------------------------------------------------------
% Need to find a way to decrease search through appointment file! Right now
% we look at everyone and compare First and Last Name.  Since the
% information on the calendar is equivalent to the online system,
% these fields should match for each subject.  If we have duplicates, then
% Vanessa can add phone number matching to the script.  We place the
% current first and last name in a deblanked variable instead of
% referencing them from the array each time so we can easily calculate the
% length without blank spaces.

for i=1:length(FirstNames)
    for k=1:length(APPTS)
        currentfirst = deblank(FirstNames{i});
        currentlast = deblank(LastNames{i});
        if length(APPTS(k).First) >= length(currentfirst)
            if strcmp(currentfirst,deblank(APPTS(k).First(1:length(currentfirst))))
                if length(APPTS(k).Last) >= length(currentlast)
                    if strcmp(currentlast,deblank(APPTS(k).Last(1:length(currentlast))))
                        APPTS(k).Phone = deblank(Phones{i});
                        APPTS(k).Text = Txt{i};
                        APPTS(k).Carrier = Carriers{i};
                        APPTS(k).Email = deblank(Emails{i});
                    end
                end
            end
        end
    end
end

clear currentfirst currentlast

%--------------------------------------------------------------------------
% Send confirmation emails
%--------------------------------------------------------------------------

% Cycle through the participants in the array, and if the appointment was
% made the previous day (since this script runs in the wee hours of the
% morning) we want to send a confirmation email with directions attached.

yesterday = today -1;

for i=1:size(APPTS,2)
    if (datenum(APPTS(i).Created) == yesterday)
            % -------------------------------------------------------------
            % FIRST SEND EMAIL
            %--------------------------------------------------------------
            % If the subject has an email, we send a confirmation email
            if isempty(APPTS(i).Email)==0
                    sendmail(APPTS(i).Email,[ 'Laboratory of Neurogenetics - ' cal{v} ' Appointment Confirmation' ],[ APPTS(i).First ', this is a confirmation of your ' cal{v} ' session appointment on ' datestr(APPTS(i).Appointment,'mmm dd, yyyy') ' at ' APPTS(i).Time '. For your appointment, please meet the experimenter at ' meetingloc{v} '. Appointment details and directions are attached.' ],reminder_directions);
            else
                    % We will want to know about this error, so we save the
                    % subject information to an array, to be emailed later.
                    APPT_ERRORS(email_count+1) = APPTS(i);
            end
    end
end

%--------------------------------------------------------------------------
% Update sending log
%--------------------------------------------------------------------------
% Initialize and print to file
    lid = fopen('CONFIRMATION_LOG.txt', 'a');

% List the headings if the file is just being created
if exist('CONFIRMATION_LOG.txt','file')==0
    fprintf(lid, 'Date,Calendar,Appt_Days_Away,First,Last,Email,Phone,Appointment,Time,Text,Carrier,');
end

for i=1:numel(APPTS)
    fprintf(lid,'\n%s', [ date ',' ]');
    fprintf(lid,'%s', [ cal{v} ',' ]');
    fprintf(lid,'%s', [ APPTS(i).First ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Last ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Email ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Phone ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Appointment ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Time ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Text ',' ]');
    fprintf(lid,'%s', APPTS(i).Carrier);
end
    fclose(lid);

end

clear i Phones Txt Carriers Emails FirstNames LastNames

%--------------------------------------------------------------------------
% Email to send if there are errors in reading the calendar or sending
% brains
%--------------------------------------------------------------------------

if exist('APPT_ERRORS','var')
    save('APPT_ERRORS','APPTS.mat');
    if exist('contactemail','var')
        sendmail(contactemail,'Message from Rem_Email.m',[  'The script had subjects with missing emails on ' date ' while sending out confirmation emails for the ' cal{v} ' calendar. The attached mat file contains these subjects!'],'APPTS.mat');
    end
end

% Exit from matlab to run the next script
exit

end

## rem_email.m
function rem_email(days,cal,sendtxt,sendemail,contactemail)

% REM_EMAIL
% Vanessa Sochat
%
% This series of scripts can be run to download appointment data from the
% lab calendar and send reminder emails at the time specified. Emails
% sent are recorded
%
% -------------------------------------------------------------------------
% VARIABLES:
% days: This is the number of days in advance that the reminder emails
% will be sent. (1 = 24 hrs, 2 = 48 hrs, etc)
%
% calendars: This is the calendar name that the reminders will be
% sent to, for each of the times indicated.  This can currently be
% "Computer" or "Imaging."
%
% sendtxt: 'yes' indicates we want to send a text message, no means no!
%
% sendemail: 'yes' indicates we want to send an email, no means no!
%
% contactemail:(optional) An email address that you want to be notified in
% the case of error
%
% -------------------------------------------------------------------------
% DEPENDENCY:
% For the script to work, it must have access to each of the appointment
% private calendars (URL's hard coded), and the data in the calendar must
% have the user email as the first thing in the Description field, like so
%
% Name: Jane Doe
% Phone: (999) 999-9999
% E-mail: jane.doe@duke.edu
%
% poozie.mat must be in the same folder it is running from
%
% schedule.csv: Downloaded by the batch script just before running
% the matlab script - this file contains all subject specific info that is
% used to look up an individual based on name.
%--------------------------------------------------------------------------
% OUTPUT:
% A temporary file of appointment info for each calendar is saved, but
% deleted when the script finishes running.  A log is updated with emails
% that were successfully sent.  All files are located under
% Y:/Scripts/Appointments
% -------------------------------------------------------------------------

%--------------------------------------------------------------------------
% Set up mail credentials
%--------------------------------------------------------------------------

load poozie.mat
email_count=0;

% Path to the reminder and directions sheet
reminder_directions = 'Y:/Scripts/Appointments/Reminder_and_Directions.pdf';
% Then this code will set up the preferences properly:
setpref('Internet','E_mail',poozie);
setpref('Internet','SMTP_Server','smtp.gmail.com');
setpref('Internet','SMTP_Username',poozie);
setpref('Internet','SMTP_Password',pooziepa);
props = java.lang.System.getProperties;
props.setProperty('mail.smtp.auth','true');
props.setProperty('mail.smtp.socketFactory.class', 'javax.net.ssl.SSLSocketFactory');
props.setProperty('mail.smtp.socketFactory.port','465');


%--------------------------------------------------------------------------
% Read in appointment file (schedule.csv) downloaded from server
%--------------------------------------------------------------------------

% If the file exists, read it in.  If it doesn't, exit with an error,
% record error to the log, and email Vanessa about error.

if exist('schedule.csv','file')
    fid = fopen('schedule.csv');
else
    % Initialize and print to file
    fid = fopen('ERROR_LOG.txt', 'a');
    fprintf(fid, 'Date: ');
    fprintf(fid,'%s\n', date');
    fprintf(fid, 'Schedule file does not exist! Check download.');
    fclose(fid);
    % If the user has provided an email, alert that email of the failure:
    if exist('contactemail','var')
        sendmail(contactemail,'Message from Rem_Email.m',[  'The script exited with error on ' date ' while sending out ' days ' day reminders for the ' calendar ' calendar. '],'');
    end
        error('Schedule file does not exist');
end

% READ APPOINTMENT INFORMATION FROM FILE

% First read in the header fields
H = textscan(fid, '%s %s %s %s %s %s %s %s %s %s %s \n', 'delimiter', ',');
% StartTime {H1}
% EndTime (H2)
% First Name (H3)
% Last Name (H4)
% Phone (H5)
% Email (H6)
% Type (H7)
% Calendar (H8)
% Duke Unique ID (H9)
% Text Message? (H10)
% Phone Carrier (H11)

% Then read the data from the rest of the file
C = textscan(fid, '%s %s %s %s %s %s %s %s %s %s %s %s %s', 'delimiter', ',');

% StartDate {C1}
% StartTime (C2)
% EndDate (C3)
% EndTime (C4)
% First Name (C5)
% Last Name (C6)
% Phone (C7)
% Email (C8)
% Appointment Type (C9)
% Clinician (C10)
% Unique ID (C11)
% Text Message? (C12)
% Phone Carrier (C13)

% Now we convert a cell array into an array of strings so we can read each
% one, only for the fields that we are interested in.
FirstNames = C{5};
LastNames = C{6};
Phones = C{7};
Emails = C{8};
Txt = C{12};
Carriers = C{13};

fclose(fid);
clear C H fid;

%--------------------------------------------------------------------------
% Download latest appointments from calendar to file
%--------------------------------------------------------------------------

% FOR CALENDAR IN calendars (NEED TO ADD THIS LOOP HERE)

% CD to directory for saving current appointment files
cd('Y:/Scripts/Appointments/');

% Download and save the calendar data
if strcmp(cal,'Imaging')
    calie = urlwrite(schmoogie,'imaging.txt','get',{});
    meetingloc = 'Soc-Psych 07';
elseif strcmp(cal,'Computer')
    meetingloc = 'LSRC B Lobby';
    calie = urlwrite(yebya,'computer.txt','get',{});
else
    error('Incorrect specification of calendar: only accepts "Computer" and "Imaging"');
end

%--------------------------------------------------------------------------
% Read appointments from the file and save to variable
%--------------------------------------------------------------------------

% Open the subject appointment file, which was an .ical file that we open as
% a text file
fln = fopen(calie);

% Create a subject count variable
appt_count=0;

% Set the current appointment date to today, so we can stop reading the
% file when the appointments go into the past.
Appointment=date;

% Set today's date in a number format for easy comparison
today = datenum(date);

while ~feof(fln)

        % We need to make sure that we only read in appointments for today and
        % in the future, so we do a comparison between the current appointment
        % that is being read.  We use a do-->while loop so that the comparison
        % until after a subject has been

        % Read in line
        currentline = fgetl(fln);

        % Look to see if we have a date line, which starts with 'DSTART'
        if regexp(currentline, 'DTSTART', 'once');
            %if yes, pull the date and time from this line, and format
            year = currentline(9:12);
            month = currentline(13:14);
            day = currentline(15:16);
            appointment = datestr([ year ' ' month ' ' day ]);
            time = currentline(18:21);
            time = str2double(time);

            % The time is 4 hours in the future, so we subtract 4:
            time = time - 400;

            % Convert military time to standard time
            if (time > 1259)
                time = time-1200;
                period = 'pm';
            else
                if (time >= 1200) && (time <= 1259)
                    period = 'pm';
                else
                    period = 'am';
                end
            end

            % Format time with a ":" by separating the last two characters
            % from the first, and sticking them together with a ":"
            time = num2str(time);
            time_end = time(length(time)-1:length(time));
            time_beg = regexprep(time, time_end, '','once');

            % Put it all together into a user friendly format for printing
            time = [ time_beg ':' time_end ' ' period ];

            % If the appointment is from before today, we don't want to do
            % anything.
            if(today > datenum(appointment))

            else
                %Add another subject to the array if they aren't from the past
                appt_count = appt_count +1;
                APPTS(appt_count)= struct('First','','Last','','Email', '','Phone','','Appointment', appointment, 'Time', time,'Text','','Carrier','');
            end
        end

        % Look to see if we have a participant info line:
        if regexp(currentline, 'DESCRIPTION', 'once');
            % Only read the line if there is data there, meaning the length
            % is greater than 12 (the length of DESCRIPTION:)
            if length(currentline) > 12
                % If the appointment is from the past, skip it, as we did
                % above
                if (today > datenum(appointment))

                else
                    %if yes, first get rid of the 'DESCRIPTION:Name: ' section
                    currentline = regexprep(currentline, currentline(1:18), '','once');
                    % Put the first name into a variable by finding the end of it,
                    % marked by a space
                    marker = regexp(currentline, ' ', 'once');
                    name = currentline(1:marker-1);
                    currentline = regexprep(currentline, currentline(1:marker), '','once');
                    % Put the last name into a variable by finding the end,
                    % marked by a space
                    marker = regexp(currentline, ' ', 'once');
                    lastname = currentline(1:marker-1);
                    % Add name to the data structure
                    APPTS(appt_count).First = deblank(name);
                    APPTS(appt_count).Last = deblank(lastname);

                end
            end
        end
        % Take in the name from the summary field, in case we need it
        if regexp(currentline, 'SUMMARY', 'once');
            currentline = regexprep(currentline, currentline(1:8), '','once');
            % Put the first name into a variable by finding the end of it,
            % marked by a space
            marker = regexp(currentline, ' ', 'once');
            name = currentline(1:marker-1);
            currentline = regexprep(currentline, currentline(1:marker), '','once');
            % Put the last name into a variable by finding the end,
            % marked by a space
            marker = regexp(currentline, ' ', 'once');
                if isempty(marker)
                    lastname = currentline;
                else
                    lastname = currentline(1:marker-1);
                end

                % In the case that the name was not present in the
                % DESCRIPTION, we can get it from the Summary!
                if isempty(APPTS(appt_count).First)
                    APPTS(appt_count).First = deblank(name);
                end
                if isempty(APPTS(appt_count).Last)
                    APPTS(appt_count).Last = deblank(lastname);
                end
        end
end

%--------------------------------------------------------------------------
% Find rest of subject info by reading from Appointment file
%--------------------------------------------------------------------------
% Need to find a way to decrease search through appointment file! Right now
% we look at everyone and compare First and Last Name.  Since the
% information on the calendar is equivalent to the online system,
% these fields should match for each subject.  If we have duplicates, then
% Vanessa can add phone number matching to the script.  We place the
% current first and last name in a deblanked variable instead of
% referencing them from the array each time so we can easily calculate the
% length without blank spaces.

for i=1:length(FirstNames)
    for k=1:length(APPTS)
        currentfirst = deblank(FirstNames{i});
        currentlast = deblank(LastNames{i});
        if length(APPTS(k).First) >= length(currentfirst)
            if strcmp(currentfirst,deblank(APPTS(k).First(1:length(currentfirst))))
                if length(APPTS(k).Last) >= length(currentlast)
                    if strcmp(currentlast,deblank(APPTS(k).Last(1:length(currentlast))))
                        APPTS(k).Phone = deblank(Phones{i});
                        APPTS(k).Text = Txt{i};
                        APPTS(k).Carrier = Carriers{i};
                        APPTS(k).Email = deblank(Emails{i});
                    end
                end
            end
        end
    end
end

clear currentfirst currentlast i Phones Txt Carriers Emails FirstNames LastNames

%--------------------------------------------------------------------------
% Send reminder emails
%--------------------------------------------------------------------------

% Cycle through the participants in the array, and if the appointment is
% within the user specified number of days, send a reminder email with
% directions attached.

% Create date (x days away from today) to compare to.  If the participant
% has an appointment on this day, he/she should receive a reminder about it
% today!
comparedate = today + days;

for i=1:size(APPTS,2)
    if (datenum(APPTS(i).Appointment) == comparedate)
            % -------------------------------------------------------------
            % FIRST SEND EMAIL
            %--------------------------------------------------------------
            if strcmp(sendemail,'yes')
                % we look at the email field to make sure that it isn't
                % blank.  If it is, this means that there was no match for
                % the subject found in the database
                if isempty(APPTS(i).Email)==0
                    sendmail(APPTS(i).Email,[ 'Laboratory of Neurogenetics - ' cal ' Appointment Reminder' ],[ APPTS(i).First ', this is a reminder about your ' cal ' session appointment on ' datestr(APPTS(i).Appointment,'mmm dd, yyyy') ' at ' APPTS(i).Time '. Please come to ' meetingloc ' and see the attached reminder and directions sheet for location details about your appointment.' ],reminder_directions);
                else
                    % We will want to know about this error, so we save the
                    % subject information to an array, to be emailed later.
                    APPT_ERRORS(email_count+1) = APPTS(i);
                end
            end

            % -------------------------------------------------------------
            % SECOND SEND TEXT
            %--------------------------------------------------------------
            if strcmp(sendtxt,'yes')
                if strcmp(APPTS(i).Text,'yes')
                    send_text_message(APPTS(i).Phone,APPTS(i).Carrier, [ cal 'Appointment Reminder' ],[ cal ' appointment reminder: ' datestr(APPTS(i).Appointment,'mmm dd, yyyy') ' at ' APPTS(i).Time ' at ' meetingloc ]);
                end
            end
    end
end

%--------------------------------------------------------------------------
% Update sending log
%--------------------------------------------------------------------------
% Initialize and print to file
    lid = fopen('LOG.txt', 'a');

% List the headings if the file is just being created
if exist('LOG.txt','file')==0
    fprintf(lid, 'Date,Calendar,Appt_Days_Away,First,Last,Email,Phone,Appointment,Time,Text,Carrier,');
end

for i=1:numel(APPTS)
    fprintf(lid,'\n%s', [ date ',' ]');
    fprintf(lid,'%s', [ cal ',' ]');
    fprintf(lid,'%s', [ days ',' ]');
    fprintf(lid,'%s', [ APPTS(i).First ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Last ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Email ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Phone ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Appointment ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Time ',' ]');
    fprintf(lid,'%s', [ APPTS(i).Text ',' ]');
    fprintf(lid,'%s', APPTS(i).Carrier);
end
    fclose(lid);

%--------------------------------------------------------------------------
% Email to send if there are errors in reading the calendar or sending
% brains
%--------------------------------------------------------------------------

if exist('APPT_ERRORS','var')
    save('APPT_ERRORS','APPTS.mat');
    if exist('contactemail','var')
        sendmail(contactemail,'Message from Rem_Email.m',[  'The script had subjects with missing emails on ' date ' while sending out ' days ' day reminders for the ' calendar ' calendar. The attached mat file contains these subjects!'],'APPTS.mat');
    end
end

% Exit from matlab to run the next script
exit

end

## send_brains.m
function send_brains()
% SEND BRAIN IMAGES (send_brains.m)
% Vanessa Sochat
%
% This script takes in a list of subjects processed in SPM, creates a brain
% images zip with two .JPG images to send to the subject, and sends it.
%__________________________________________________________________________
%
% DEPENDENCIES: You need to have the crop.m script in the same folder for
% this to work: http://vsoch.com/LONG/Vanessa/MATLAB/Send%20Brains/crop.m
%
% SUBJECT ID: This script is set up to work with DNS data - it is expecting
% IDs to have the format (DATE)_(SUBJECT ID).  As the subject output images
% are named with the five numbers after the "_" (representing the subject
% ID) - this is the format that the script is expecting.  If your subject
% IDs do not fit this format, you can nix the section that goes through the
% processed subject names and creates a string of modified IDs and just use
% the processed subject list raw without any changes to compare the files
% variable list to.
%
%__________________________________________________________________________
%
% USAGE: send_brains()
% no input variables are required as the program takes them into a GUI.
%__________________________________________________________________________
%
% ORGANIZATION: You should maintain the following file structure:
% Output images under DNS.01\Graphics\Brain Images
% Input Data: We will be using the processed highres under "anat"
% sdns01-005-00001-000001-01.img, to create the image from.
%__________________________________________________________________________
%
% This script works by....
%   1. Creating the list of potential sendees - whoever has been newly
%   processed that week and does not have a brain image created yet.
%   2. The script then presents this list to the user, and asks if he/she
%   would like to delete any participants. This is important because we
%   could have a test folder under Processed, or potentially a participant
%   that we don't want to send to. To delete a participant, the user simply
%   enters the ID into the GUI, and then the script presents the user with
%   the new list. There is no negative consequence of making a typo and
%   entering an incorrect ID - the script will not find the ID in the list,
%   and will present the identical list to the user, and he/she can enter
%   the ID again.
%   3. Next, the script looks for the processed anatomical in the subject's
%   anat directory under Processed. This image will normally always have
%   the same name - however in rare cases when the name is different,
%   for whatever reason, the script will not find the highres, and will
%   present the user with a GUI to select the image that he/she would like
%   to use for that participant. It then prepares two slice views of the
%   highres, crops them, puts them together as a zip, moves the zip to the
%   Graphics/Brain Images folder, and cleans up the old files.
%   4. Once all brain image zips have been created, the script prompts the
%   user if he/she wants to send a brain image for each subject, and asks
%   the user to enter the email. This process is fairly rapid and easy.
%   In the case that the user mistypes an email, the easiest thing to do
%   is delete the output image, and quickly run the script again.
%   5. As each address in entered, the script sends the email directly from
%   MATLAB.
%__________________________________________________________________________
%__________________________________________________________________________


%-Global Variables
%-----------------------------------------------------------------------
fprintf('SEND_BRAIN.M Alpha\n Vanessa Sochat\n August, 2010\n');

% Here the user specifies the experiment directory
homedir = spm_select(1,'dir','Select top of experiment directory','','N:');

% Here the user specifies the output directory
output = spm_select(1,'dir','Select output directory','',[ homedir 'Graphics\' ] );

% Here we set the Processed directory
processed_dir = horzcat(homedir,'Analysis\SPM\Processed\');

% Add the path to the crop script
addpath(genpath('N:\DNS.01\Scripts\MATLAB\Vanessa\Send Brains'));

%-Identify subject list to make brain images for
%-----------------------------------------------------------------------
% Here the script compares the subjects in the "Processed" folder (meaning
% they have been processed and we can send a brain image) to the brain
% images in the output folder.  The subject IDs that appear in the Processed
% folder but not the output folder are saved into a variable as they need
% to have brain images sent.  Then, the user is allowed to delete subjects
% or text from the string, as it could be likely that there is a TEST
% folder or file in the processed directory that isn't a subject to send
% brain images to.

% First get the processed subjects
cd(processed_dir)
processed = [ ls ];

% And then we grab the subject IDs who have had brain images.
cd(output);
files = [ ls ];

% Initialize brain_list variables
brain_list = '';

% We start at the third element because the first two are "." and ".."
for c = 3:size(processed,1)

    % The subject ID always starts at the 10th spot, and ends at te 15th, so we
    % use those coordinates to pull the subject IDs fromn the processed variable.
    % You will need to change this if you have a different format, or you could
    % just get rid of it completely and use the entire subject ID for the image names.
    current_processed = processed(c,:);


    % By default, add_var starts out as 'yes' and only gets changed to
        % no if we find a matched subject ID.
        add_var = 'yes';

        % VANESSA - MIGHT WANT TO ADD SOME SORT OF BREAK IF A MATCH IS
        % FOUND, SO DON'T KEEP SEARCHING ONCE IS FOUND!
        for i = 1:size(files,1)
            % We take the first 5 characters of the file name, which is the
            % subject's ID
            subject = files(i,1:5);

            if strcmp(current_processed(10:14),subject)
                % If the processed subject can be found under the output files
                % list, then the brain image has already been processed and we
                % exit the loop without adding anything
                add_var = 'no';
            end
        end

    % After cycling through the list of brain images already made, we only
    % flag the subject as needing an image if the add_var is set to "yes" -
    % meaning that no match was ever found.
    if strcmp(add_var,'yes')
        brain_list = [ brain_list;current_processed ];
    end

    % and now we move on to the next processed subject at the start of the
    % loop
end

% Clean up
clear current_processed subject

fprintf('%s\n','The list of subjects that need brain images is...');
selections = listdlg('PromptString','Select Subjects to send to:','SelectionMode','multiple','ListString',brain_list);

% Pull the user selections from the brain list, and put them in the
% temp_list

add_count = 0;
for j = 1:size(selections,2)
    add_count = add_count +1;
    temp_list{add_count} = deblank(brain_list(selections(j),:));
end

clear selections

%-Create brain images
%-----------------------------------------------------------------------
% This part of the script goes to the subject's anatomical directory,
% creates the brain image, and saves it to the output directory.

% Initialize graphic viewer
spm_figure('GetWin','Graphics');
clear global st

% Read in logo and prepare file array (to make zip) just once!
I = imread('http://www.haririlab.com/img/logo_small.jpg');
I = imresize(I, 2);
imagefiles{1}='slices.JPG';
imagefiles{2}='sagittal.JPG';

for i=1:size(temp_list,2)
    subject = temp_list{i};

    % CD to subject's anatomical folder
    if exist(horzcat(processed_dir,subject,'/anat/'),'dir')
        cd(horzcat(processed_dir,subject,'/anat/'));

        % If the default anatomical/highres exists, we use that
        if exist(horzcat(processed_dir,subject,'/anat/sdns01-0005-00001-000001-01.img'),'file');
            anat = horzcat(processed_dir,subject,'/anat/sdns01-0005-00001-000001-01.img');

                % Create slices view and save...
                SO=slover();
                SO.img(1).vol=spm_vol(anat);
                SO.slices = [-36:2:70];
                SO=paint(SO);

                % Add logo to slices image and save
                image(I)
                axis off
                print -dtiff -noui slices.JPG
                crop('slices.JPG');

                % Print sagittal view
                SO=slover();
                SO.img(1).vol=spm_vol(anat);
                SO.slices = [-2:10:52];
                SO.transform = 'sagittal';
                SO=paint(SO);
                axis off
                print -dtiff -noui sagittal.JPG
                crop('sagittal.JPG');

                % Prepare zip of two files
                zip('brain',imagefiles)

                % Save final image to output directory
                copyfile('brain.ZIP',[ output,subject(10:14),'.ZIP' ]);
                delete brain.ZIP
                delete slices.JPG
                delete sagittal.JPG
                clear SO
        else
            % If not, we give the user the option to select the file
            h = msgbox([ 'Default highres does not exist for ' subject '!' ],'File Not Found','warn');
            uiwait(h);

            files = [ ls ];

            [ selection use_anat ] = listdlg('PromptString','Select file, or CANCEL to skip','SelectionMode','single','ListString',files);

            if use_anat == 1

                anat = files(selection,:);

                % Create slices view and save...
                SO=slover();
                SO.img(1).vol=spm_vol(anat);
                SO.slices = [-36:2:70];
                SO=paint(SO);

                % Add logo to slices image and save
                image(I)
                axis off
                print -dtiff -noui slices.JPG
                crop('slices.JPG');

                % Print sagittal view
                SO=slover();
                SO.img(1).vol=spm_vol(anat);
                SO.slices = [-2:10:52];
                SO.transform = 'sagittal';
                SO=paint(SO);
                axis off
                print -dtiff -noui sagittal.JPG
                crop('sagittal.JPG');

                % Prepare zip of two files
                zip('brain',imagefiles)

                % Save final image to output directory
                copyfile('brain.ZIP',[ output,subject(10:14),'.ZIP' ]);
                delete brain.ZIP
                delete slices.JPG
                delete sagittal.JPG
                clear SO

            else
                fprintf('%s%s%s\n','Please take not that subject ',subject,' has been skipped!');
            end
        end
    else
        fprintf('%s%s%s\n','Subject ',subject,' does not have an anat folder under Processed!')
    end
end

%-Send Brain Images
%-----------------------------------------------------------------------
% This part of the script goes to the output directory and sends an email
% for each subject
cd(output);

% Must be in the same folder as the script
load poozie.mat

% Then this code will set up the preferences properly:
setpref('Internet','E_mail',poozie);
setpref('Internet','SMTP_Server','smtp.gmail.com');
setpref('Internet','SMTP_Username',poozie);
setpref('Internet','SMTP_Password',pooziepa);
props = java.lang.System.getProperties;
props.setProperty('mail.smtp.auth','true');
props.setProperty('mail.smtp.socketFactory.class', 'javax.net.ssl.SSLSocketFactory');
props.setProperty('mail.smtp.socketFactory.port','465');

for i=1:size(temp_list,2)
    subject = temp_list{i};
    send_var=spm_input([ 'Send image to:',subject(10:14),'?' ],1,'Yes|No');
    if strcmp(send_var,'Yes')
        email = spm_input([ subject(10:14),' email address:' ],2,'s','',1);

        % Check to see if the brain image exists, just in case!
        if exist([ subject(10:14),'.ZIP' ],'file')
            brain_image=[ subject(10:14),'.ZIP' ];
            % Send the email. Note that the first input is the address!
            sendmail(email,'Laboratory of Neurogenetics - Brain Image','Attached, please find an image of your brain.  This image is intended for personal use only. The image is NOT intended as and should NOT be used as a substitute for medical evaluation.',brain_image);
        else
            fprintf('%s%s/n',subject(10:14),'.ZIP cannot be found! Brain image not sent!');
        end
    end
end

fprintf('%s\n','Done sending brain images!');

end
	function confirmation_email(contactemail)

	% CONFIRMATION_EMAIL
	% Vanessa Sochat
	%
	% This script sends confirmation emails for imaging and battery appointments
	% added to the calendar the previous day.
	%
	% -------------------------------------------------------------------------
	% VARIABLES:
	%
	% contactemail: An email address that you want to be notified in
	% the case of error
	%
	% -------------------------------------------------------------------------
	% DEPENDENCY:
	% For the script to work, it must have access to each of the appointment
	% private calendars (URL's hard coded), and the data in the calendar must
	% have the user email as the first thing in the Description field, like so
	%
	% Name: Jane Doe
	% Phone: (999) 999-9999
	% E-mail: jane.doe@duke.edu
	%
	% poozie.mat must be in the same folder it is running from
	%
	% schedule.csv: Downloaded by the batch script just before running
	% the matlab script - this file contains all subject specific info that is
	% used to look up an individual based on name.
	%--------------------------------------------------------------------------
	% OUTPUT:
	% A log of confirmation email info is saved, and all files are located
	% under:
	%
	% Y:/Scripts/Appointments
	% -------------------------------------------------------------------------

	%--------------------------------------------------------------------------
	% Set up mail credentials
	%--------------------------------------------------------------------------

	load poozie.mat
	email_count=0;

	% Path to the reminder and directions sheet
	reminder_directions = 'Y:/Scripts/Appointments/Reminder_and_Directions.pdf';
	% Then this code will set up the preferences properly:
	setpref('Internet','E_mail',poozie);
	setpref('Internet','SMTP_Server','smtp.gmail.com');
	setpref('Internet','SMTP_Username',poozie);
	setpref('Internet','SMTP_Password',pooziepa);
	props = java.lang.System.getProperties;
	props.setProperty('mail.smtp.auth','true');
	props.setProperty('mail.smtp.socketFactory.class', 'javax.net.ssl.SSLSocketFactory');
	props.setProperty('mail.smtp.socketFactory.port','465');


	%--------------------------------------------------------------------------
	% Read in appointment file (schedule.csv) downloaded from server
	%--------------------------------------------------------------------------

	% If the file exists, read it in. If it doesn't, exit with an error,
	% record error to the log, and email Vanessa about error.

	if exist('schedule.csv','file')
	fid = fopen('schedule.csv');
	else
	% Initialize and print to file
	fid = fopen('ERROR_LOG.txt', 'a');
	fprintf(fid, 'Date: ');
	fprintf(fid,'%s\n', date');
	fprintf(fid, 'Schedule file does not exist! Check download.');
	fclose(fid);
	% If the user has provided an email, alert that email of the failure:
	if exist('contactemail','var')
	sendmail(contactemail,'Message from Rem_Email.m',[ 'The script exited with error on ' date ' while sending out ' days ' day reminders for the ' calendar ' calendar. '],'');
	end
	error('Schedule file does not exist');
	end

	% READ APPOINTMENT INFORMATION FROM FILE

	% First read in the header fields
	H = textscan(fid, '%s %s %s %s %s %s %s %s %s %s %s \n', 'delimiter', ',');
	% StartTime {H1}
	% EndTime (H2)
	% First Name (H3)
	% Last Name (H4)
	% Phone (H5)
	% Email (H6)
	% Type (H7)
	% Calendar (H8)
	% Duke Unique ID (H9)
	% Text Message? (H10)
	% Phone Carrier (H11)

	% Then read the data from the rest of the file
	C = textscan(fid, '%s %s %s %s %s %s %s %s %s %s %s %s %s', 'delimiter', ',');

	% StartDate {C1}
	% StartTime (C2)
	% EndDate (C3)
	% EndTime (C4)
	% First Name (C5)
	% Last Name (C6)
	% Phone (C7)
	% Email (C8)
	% Appointment Type (C9)
	% Clinician (C10)
	% Unique ID (C11)
	% Text Message? (C12)
	% Phone Carrier (C13)

	% Now we convert a cell array into an array of strings so we can read each
	% one, only for the fields that we are interested in.
	FirstNames = C{5};
	LastNames = C{6};
	Phones = C{7};
	Emails = C{8};
	Txt = C{12};
	Carriers = C{13};

	fclose(fid);
	clear C H fid;

	%--------------------------------------------------------------------------
	% Download latest appointments from imaging and computer calendar to file
	%--------------------------------------------------------------------------

	% CD to directory for saving current appointment files
	cd('Y:/Scripts/Appointments/');

	% Download and save the calendar data, if it doesn't already exist in the
	% folder (since the reminder emails are sent just before and haven't been
	% deleted by the batch script, these files should already exist!)

	if exist('imaging.txt','file')==0
	calie{1} = urlwrite(schmoogie,'imaging.txt','get',{});
	else
	calie{1} = 'imaging.txt';
	end
	meetingloc{1} = 'Soc-Psych 07';
	cal{1} = 'Imaging';

	if exist('computer.txt','file')==0
	calie{2} = urlwrite(yebya,'computer.txt','get',{});
	else
	calie{2} = 'computer.txt';
	end
	meetingloc{2} = 'LSRC B Lobby';
	cal{2} = 'Computer';

	%--------------------------------------------------------------------------
	% Read appointments from the file and save to variable
	%--------------------------------------------------------------------------

	% Open the subject appointment file, which was an .ical file that we open as
	% a text file

	for v=1:2

	fln = fopen(calie{v});

	% Create a subject count variable
	appt_count=0;

	% Set the current appointment date to today, so we can stop reading the
	% file when the appointments go into the past.
	Appointment=date;

	% Set today's date in a number format for easy comparison
	today = datenum(date);

	while ~feof(fln)

	% We need to make sure that we only read in appointments for today and
	% in the future, so we do a comparison between the current appointment
	% that is being read. We use a do-->while loop so that the comparison
	% until after a subject has been

	% Read in line
	currentline = fgetl(fln);

	% Look to see if we have a date line, which starts with 'DSTART'
	if regexp(currentline, 'DTSTART', 'once');
	%if yes, pull the date and time from this line, and format
	year = currentline(9:12);
	month = currentline(13:14);
	day = currentline(15:16);
	appointment = datestr([ year ' ' month ' ' day ]);
	time = currentline(18:21);
	time = str2double(time);

	% The time is 4 hours in the future, so we subtract 4:
	time = time - 400;

	% Convert military time to standard time
	if (time > 1259)
	time = time-1200;
	period = 'pm';
	else
	if (time >= 1200) && (time <= 1259)
	period = 'pm';
	else
	period = 'am';
	end
	end

	% Format time with a ":" by separating the last two characters
	% from the first, and sticking them together with a ":"
	time = num2str(time);
	time_end = time(length(time)-1:length(time));
	time_beg = regexprep(time, time_end, '','once');

	% Put it all together into a user friendly format for printing
	time = [ time_beg ':' time_end ' ' period ];

	% If the appointment is from before today, we don't want to do
	% anything.
	if(today > datenum(appointment))

	else
	%Add another subject to the array if they aren't from the past
	appt_count = appt_count +1;
	APPTS(appt_count)= struct('First','','Last','','Email', '','Phone','','Appointment', appointment, 'Time', time,'Text','','Carrier','','Created','');
	end
	end

	% Look to see if we have a date created line, which starts with 'CREATED'
	if regexp(currentline, 'CREATED', 'once');
	%if yes, pull the date and time from this line, and format
	create_year = currentline(9:12);
	create_month = currentline(13:14);
	create_day = currentline(15:16);
	created = datestr([ create_year ' ' create_month ' ' create_day ]);

	% If the appointment is from before today, we don't want to do
	% anything.
	if(today > datenum(appointment))

	else
	APPTS(appt_count).Created = created;
	end
	end

	% Look to see if we have a participant info line:
	if regexp(currentline, 'DESCRIPTION', 'once');
	% Only read the line if there is data there, meaning the length
	% is greater than 12 (the length of DESCRIPTION:)
	if length(currentline) > 12
	% If the appointment is from the past, skip it, as we did
	% above
	if (today > datenum(appointment))

	else
	%if yes, first get rid of the 'DESCRIPTION:Name: ' section
	currentline = regexprep(currentline, currentline(1:18), '','once');
	% Put the first name into a variable by finding the end of it,
	% marked by a space
	marker = regexp(currentline, ' ', 'once');
	name = currentline(1:marker-1);
	currentline = regexprep(currentline, currentline(1:marker), '','once');
	% Put the last name into a variable by finding the end,
	% marked by a space
	marker = regexp(currentline, ' ', 'once');
	lastname = currentline(1:marker-1);
	% Add name to the data structure
	APPTS(appt_count).First = deblank(name);
	APPTS(appt_count).Last = deblank(lastname);

	end
	end
	end
	% Take in the name from the summary field, in case we need it
	if regexp(currentline, 'SUMMARY', 'once');
	currentline = regexprep(currentline, currentline(1:8), '','once');
	% Put the first name into a variable by finding the end of it,
	% marked by a space
	marker = regexp(currentline, ' ', 'once');
	name = currentline(1:marker-1);
	currentline = regexprep(currentline, currentline(1:marker), '','once');
	% Put the last name into a variable by finding the end,
	% marked by a space
	marker = regexp(currentline, ' ', 'once');
	if isempty(marker)
	lastname = currentline;
	else
	lastname = currentline(1:marker-1);
	end

	% In the case that the name was not present in the
	% DESCRIPTION, we can get it from the Summary!
	if isempty(APPTS(appt_count).First)
	APPTS(appt_count).First = deblank(name);
	end
	if isempty(APPTS(appt_count).Last)
	APPTS(appt_count).Last = deblank(lastname);
	end
	end
	end

	%--------------------------------------------------------------------------
	% Find rest of subject info by reading from Appointment file
	%--------------------------------------------------------------------------
	% Need to find a way to decrease search through appointment file! Right now
	% we look at everyone and compare First and Last Name. Since the
	% information on the calendar is equivalent to the online system,
	% these fields should match for each subject. If we have duplicates, then
	% Vanessa can add phone number matching to the script. We place the
	% current first and last name in a deblanked variable instead of
	% referencing them from the array each time so we can easily calculate the
	% length without blank spaces.

	for i=1:length(FirstNames)
	for k=1:length(APPTS)
	currentfirst = deblank(FirstNames{i});
	currentlast = deblank(LastNames{i});
	if length(APPTS(k).First) >= length(currentfirst)
	if strcmp(currentfirst,deblank(APPTS(k).First(1:length(currentfirst))))
	if length(APPTS(k).Last) >= length(currentlast)
	if strcmp(currentlast,deblank(APPTS(k).Last(1:length(currentlast))))
	APPTS(k).Phone = deblank(Phones{i});
	APPTS(k).Text = Txt{i};
	APPTS(k).Carrier = Carriers{i};
	APPTS(k).Email = deblank(Emails{i});
	end
	end
	end
	end
	end
	end

	clear currentfirst currentlast

	%--------------------------------------------------------------------------
	% Send confirmation emails
	%--------------------------------------------------------------------------

	% Cycle through the participants in the array, and if the appointment was
	% made the previous day (since this script runs in the wee hours of the
	% morning) we want to send a confirmation email with directions attached.

	yesterday = today -1;

	for i=1:size(APPTS,2)
	if (datenum(APPTS(i).Created) == yesterday)
	% -------------------------------------------------------------
	% FIRST SEND EMAIL
	%--------------------------------------------------------------
	% If the subject has an email, we send a confirmation email
	if isempty(APPTS(i).Email)==0
	sendmail(APPTS(i).Email,[ 'Laboratory of Neurogenetics - ' cal{v} ' Appointment Confirmation' ],[ APPTS(i).First ', this is a confirmation of your ' cal{v} ' session appointment on ' datestr(APPTS(i).Appointment,'mmm dd, yyyy') ' at ' APPTS(i).Time '. For your appointment, please meet the experimenter at ' meetingloc{v} '. Appointment details and directions are attached.' ],reminder_directions);
	else
	% We will want to know about this error, so we save the
	% subject information to an array, to be emailed later.
	APPT_ERRORS(email_count+1) = APPTS(i);
	end
	end
	end

	%--------------------------------------------------------------------------
	% Update sending log
	%--------------------------------------------------------------------------
	% Initialize and print to file
	lid = fopen('CONFIRMATION_LOG.txt', 'a');

	% List the headings if the file is just being created
	if exist('CONFIRMATION_LOG.txt','file')==0
	fprintf(lid, 'Date,Calendar,Appt_Days_Away,First,Last,Email,Phone,Appointment,Time,Text,Carrier,');
	end

	for i=1:numel(APPTS)
	fprintf(lid,'\n%s', [ date ',' ]');
	fprintf(lid,'%s', [ cal{v} ',' ]');
	fprintf(lid,'%s', [ APPTS(i).First ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Last ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Email ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Phone ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Appointment ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Time ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Text ',' ]');
	fprintf(lid,'%s', APPTS(i).Carrier);
	end
	fclose(lid);

	end

	clear i Phones Txt Carriers Emails FirstNames LastNames

	%--------------------------------------------------------------------------
	% Email to send if there are errors in reading the calendar or sending
	% brains
	%--------------------------------------------------------------------------

	if exist('APPT_ERRORS','var')
	save('APPT_ERRORS','APPTS.mat');
	if exist('contactemail','var')
	sendmail(contactemail,'Message from Rem_Email.m',[ 'The script had subjects with missing emails on ' date ' while sending out confirmation emails for the ' cal{v} ' calendar. The attached mat file contains these subjects!'],'APPTS.mat');
	end
	end

	% Exit from matlab to run the next script
	exit

	end
	function rem_email(days,cal,sendtxt,sendemail,contactemail)

	% REM_EMAIL
	% Vanessa Sochat
	%
	% This series of scripts can be run to download appointment data from the
	% lab calendar and send reminder emails at the time specified. Emails
	% sent are recorded
	%
	% -------------------------------------------------------------------------
	% VARIABLES:
	% days: This is the number of days in advance that the reminder emails
	% will be sent. (1 = 24 hrs, 2 = 48 hrs, etc)
	%
	% calendars: This is the calendar name that the reminders will be
	% sent to, for each of the times indicated. This can currently be
	% "Computer" or "Imaging."
	%
	% sendtxt: 'yes' indicates we want to send a text message, no means no!
	%
	% sendemail: 'yes' indicates we want to send an email, no means no!
	%
	% contactemail:(optional) An email address that you want to be notified in
	% the case of error
	%
	% -------------------------------------------------------------------------
	% DEPENDENCY:
	% For the script to work, it must have access to each of the appointment
	% private calendars (URL's hard coded), and the data in the calendar must
	% have the user email as the first thing in the Description field, like so
	%
	% Name: Jane Doe
	% Phone: (999) 999-9999
	% E-mail: jane.doe@duke.edu
	%
	% poozie.mat must be in the same folder it is running from
	%
	% schedule.csv: Downloaded by the batch script just before running
	% the matlab script - this file contains all subject specific info that is
	% used to look up an individual based on name.
	%--------------------------------------------------------------------------
	% OUTPUT:
	% A temporary file of appointment info for each calendar is saved, but
	% deleted when the script finishes running. A log is updated with emails
	% that were successfully sent. All files are located under
	% Y:/Scripts/Appointments
	% -------------------------------------------------------------------------

	%--------------------------------------------------------------------------
	% Set up mail credentials
	%--------------------------------------------------------------------------

	load poozie.mat
	email_count=0;

	% Path to the reminder and directions sheet
	reminder_directions = 'Y:/Scripts/Appointments/Reminder_and_Directions.pdf';
	% Then this code will set up the preferences properly:
	setpref('Internet','E_mail',poozie);
	setpref('Internet','SMTP_Server','smtp.gmail.com');
	setpref('Internet','SMTP_Username',poozie);
	setpref('Internet','SMTP_Password',pooziepa);
	props = java.lang.System.getProperties;
	props.setProperty('mail.smtp.auth','true');
	props.setProperty('mail.smtp.socketFactory.class', 'javax.net.ssl.SSLSocketFactory');
	props.setProperty('mail.smtp.socketFactory.port','465');


	%--------------------------------------------------------------------------
	% Read in appointment file (schedule.csv) downloaded from server
	%--------------------------------------------------------------------------

	% If the file exists, read it in. If it doesn't, exit with an error,
	% record error to the log, and email Vanessa about error.

	if exist('schedule.csv','file')
	fid = fopen('schedule.csv');
	else
	% Initialize and print to file
	fid = fopen('ERROR_LOG.txt', 'a');
	fprintf(fid, 'Date: ');
	fprintf(fid,'%s\n', date');
	fprintf(fid, 'Schedule file does not exist! Check download.');
	fclose(fid);
	% If the user has provided an email, alert that email of the failure:
	if exist('contactemail','var')
	sendmail(contactemail,'Message from Rem_Email.m',[ 'The script exited with error on ' date ' while sending out ' days ' day reminders for the ' calendar ' calendar. '],'');
	end
	error('Schedule file does not exist');
	end

	% READ APPOINTMENT INFORMATION FROM FILE

	% First read in the header fields
	H = textscan(fid, '%s %s %s %s %s %s %s %s %s %s %s \n', 'delimiter', ',');
	% StartTime {H1}
	% EndTime (H2)
	% First Name (H3)
	% Last Name (H4)
	% Phone (H5)
	% Email (H6)
	% Type (H7)
	% Calendar (H8)
	% Duke Unique ID (H9)
	% Text Message? (H10)
	% Phone Carrier (H11)

	% Then read the data from the rest of the file
	C = textscan(fid, '%s %s %s %s %s %s %s %s %s %s %s %s %s', 'delimiter', ',');

	% StartDate {C1}
	% StartTime (C2)
	% EndDate (C3)
	% EndTime (C4)
	% First Name (C5)
	% Last Name (C6)
	% Phone (C7)
	% Email (C8)
	% Appointment Type (C9)
	% Clinician (C10)
	% Unique ID (C11)
	% Text Message? (C12)
	% Phone Carrier (C13)

	% Now we convert a cell array into an array of strings so we can read each
	% one, only for the fields that we are interested in.
	FirstNames = C{5};
	LastNames = C{6};
	Phones = C{7};
	Emails = C{8};
	Txt = C{12};
	Carriers = C{13};

	fclose(fid);
	clear C H fid;

	%--------------------------------------------------------------------------
	% Download latest appointments from calendar to file
	%--------------------------------------------------------------------------

	% FOR CALENDAR IN calendars (NEED TO ADD THIS LOOP HERE)

	% CD to directory for saving current appointment files
	cd('Y:/Scripts/Appointments/');

	% Download and save the calendar data
	if strcmp(cal,'Imaging')
	calie = urlwrite(schmoogie,'imaging.txt','get',{});
	meetingloc = 'Soc-Psych 07';
	elseif strcmp(cal,'Computer')
	meetingloc = 'LSRC B Lobby';
	calie = urlwrite(yebya,'computer.txt','get',{});
	else
	error('Incorrect specification of calendar: only accepts "Computer" and "Imaging"');
	end

	%--------------------------------------------------------------------------
	% Read appointments from the file and save to variable
	%--------------------------------------------------------------------------

	% Open the subject appointment file, which was an .ical file that we open as
	% a text file
	fln = fopen(calie);

	% Create a subject count variable
	appt_count=0;

	% Set the current appointment date to today, so we can stop reading the
	% file when the appointments go into the past.
	Appointment=date;

	% Set today's date in a number format for easy comparison
	today = datenum(date);

	while ~feof(fln)

	% We need to make sure that we only read in appointments for today and
	% in the future, so we do a comparison between the current appointment
	% that is being read. We use a do-->while loop so that the comparison
	% until after a subject has been

	% Read in line
	currentline = fgetl(fln);

	% Look to see if we have a date line, which starts with 'DSTART'
	if regexp(currentline, 'DTSTART', 'once');
	%if yes, pull the date and time from this line, and format
	year = currentline(9:12);
	month = currentline(13:14);
	day = currentline(15:16);
	appointment = datestr([ year ' ' month ' ' day ]);
	time = currentline(18:21);
	time = str2double(time);

	% The time is 4 hours in the future, so we subtract 4:
	time = time - 400;

	% Convert military time to standard time
	if (time > 1259)
	time = time-1200;
	period = 'pm';
	else
	if (time >= 1200) && (time <= 1259)
	period = 'pm';
	else
	period = 'am';
	end
	end

	% Format time with a ":" by separating the last two characters
	% from the first, and sticking them together with a ":"
	time = num2str(time);
	time_end = time(length(time)-1:length(time));
	time_beg = regexprep(time, time_end, '','once');

	% Put it all together into a user friendly format for printing
	time = [ time_beg ':' time_end ' ' period ];

	% If the appointment is from before today, we don't want to do
	% anything.
	if(today > datenum(appointment))

	else
	%Add another subject to the array if they aren't from the past
	appt_count = appt_count +1;
	APPTS(appt_count)= struct('First','','Last','','Email', '','Phone','','Appointment', appointment, 'Time', time,'Text','','Carrier','');
	end
	end

	% Look to see if we have a participant info line:
	if regexp(currentline, 'DESCRIPTION', 'once');
	% Only read the line if there is data there, meaning the length
	% is greater than 12 (the length of DESCRIPTION:)
	if length(currentline) > 12
	% If the appointment is from the past, skip it, as we did
	% above
	if (today > datenum(appointment))

	else
	%if yes, first get rid of the 'DESCRIPTION:Name: ' section
	currentline = regexprep(currentline, currentline(1:18), '','once');
	% Put the first name into a variable by finding the end of it,
	% marked by a space
	marker = regexp(currentline, ' ', 'once');
	name = currentline(1:marker-1);
	currentline = regexprep(currentline, currentline(1:marker), '','once');
	% Put the last name into a variable by finding the end,
	% marked by a space
	marker = regexp(currentline, ' ', 'once');
	lastname = currentline(1:marker-1);
	% Add name to the data structure
	APPTS(appt_count).First = deblank(name);
	APPTS(appt_count).Last = deblank(lastname);

	end
	end
	end
	% Take in the name from the summary field, in case we need it
	if regexp(currentline, 'SUMMARY', 'once');
	currentline = regexprep(currentline, currentline(1:8), '','once');
	% Put the first name into a variable by finding the end of it,
	% marked by a space
	marker = regexp(currentline, ' ', 'once');
	name = currentline(1:marker-1);
	currentline = regexprep(currentline, currentline(1:marker), '','once');
	% Put the last name into a variable by finding the end,
	% marked by a space
	marker = regexp(currentline, ' ', 'once');
	if isempty(marker)
	lastname = currentline;
	else
	lastname = currentline(1:marker-1);
	end

	% In the case that the name was not present in the
	% DESCRIPTION, we can get it from the Summary!
	if isempty(APPTS(appt_count).First)
	APPTS(appt_count).First = deblank(name);
	end
	if isempty(APPTS(appt_count).Last)
	APPTS(appt_count).Last = deblank(lastname);
	end
	end
	end

	%--------------------------------------------------------------------------
	% Find rest of subject info by reading from Appointment file
	%--------------------------------------------------------------------------
	% Need to find a way to decrease search through appointment file! Right now
	% we look at everyone and compare First and Last Name. Since the
	% information on the calendar is equivalent to the online system,
	% these fields should match for each subject. If we have duplicates, then
	% Vanessa can add phone number matching to the script. We place the
	% current first and last name in a deblanked variable instead of
	% referencing them from the array each time so we can easily calculate the
	% length without blank spaces.

	for i=1:length(FirstNames)
	for k=1:length(APPTS)
	currentfirst = deblank(FirstNames{i});
	currentlast = deblank(LastNames{i});
	if length(APPTS(k).First) >= length(currentfirst)
	if strcmp(currentfirst,deblank(APPTS(k).First(1:length(currentfirst))))
	if length(APPTS(k).Last) >= length(currentlast)
	if strcmp(currentlast,deblank(APPTS(k).Last(1:length(currentlast))))
	APPTS(k).Phone = deblank(Phones{i});
	APPTS(k).Text = Txt{i};
	APPTS(k).Carrier = Carriers{i};
	APPTS(k).Email = deblank(Emails{i});
	end
	end
	end
	end
	end
	end

	clear currentfirst currentlast i Phones Txt Carriers Emails FirstNames LastNames

	%--------------------------------------------------------------------------
	% Send reminder emails
	%--------------------------------------------------------------------------

	% Cycle through the participants in the array, and if the appointment is
	% within the user specified number of days, send a reminder email with
	% directions attached.

	% Create date (x days away from today) to compare to. If the participant
	% has an appointment on this day, he/she should receive a reminder about it
	% today!
	comparedate = today + days;

	for i=1:size(APPTS,2)
	if (datenum(APPTS(i).Appointment) == comparedate)
	% -------------------------------------------------------------
	% FIRST SEND EMAIL
	%--------------------------------------------------------------
	if strcmp(sendemail,'yes')
	% we look at the email field to make sure that it isn't
	% blank. If it is, this means that there was no match for
	% the subject found in the database
	if isempty(APPTS(i).Email)==0
	sendmail(APPTS(i).Email,[ 'Laboratory of Neurogenetics - ' cal ' Appointment Reminder' ],[ APPTS(i).First ', this is a reminder about your ' cal ' session appointment on ' datestr(APPTS(i).Appointment,'mmm dd, yyyy') ' at ' APPTS(i).Time '. Please come to ' meetingloc ' and see the attached reminder and directions sheet for location details about your appointment.' ],reminder_directions);
	else
	% We will want to know about this error, so we save the
	% subject information to an array, to be emailed later.
	APPT_ERRORS(email_count+1) = APPTS(i);
	end
	end

	% -------------------------------------------------------------
	% SECOND SEND TEXT
	%--------------------------------------------------------------
	if strcmp(sendtxt,'yes')
	if strcmp(APPTS(i).Text,'yes')
	send_text_message(APPTS(i).Phone,APPTS(i).Carrier, [ cal 'Appointment Reminder' ],[ cal ' appointment reminder: ' datestr(APPTS(i).Appointment,'mmm dd, yyyy') ' at ' APPTS(i).Time ' at ' meetingloc ]);
	end
	end
	end
	end

	%--------------------------------------------------------------------------
	% Update sending log
	%--------------------------------------------------------------------------
	% Initialize and print to file
	lid = fopen('LOG.txt', 'a');

	% List the headings if the file is just being created
	if exist('LOG.txt','file')==0
	fprintf(lid, 'Date,Calendar,Appt_Days_Away,First,Last,Email,Phone,Appointment,Time,Text,Carrier,');
	end

	for i=1:numel(APPTS)
	fprintf(lid,'\n%s', [ date ',' ]');
	fprintf(lid,'%s', [ cal ',' ]');
	fprintf(lid,'%s', [ days ',' ]');
	fprintf(lid,'%s', [ APPTS(i).First ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Last ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Email ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Phone ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Appointment ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Time ',' ]');
	fprintf(lid,'%s', [ APPTS(i).Text ',' ]');
	fprintf(lid,'%s', APPTS(i).Carrier);
	end
	fclose(lid);

	%--------------------------------------------------------------------------
	% Email to send if there are errors in reading the calendar or sending
	% brains
	%--------------------------------------------------------------------------

	if exist('APPT_ERRORS','var')
	save('APPT_ERRORS','APPTS.mat');
	if exist('contactemail','var')
	sendmail(contactemail,'Message from Rem_Email.m',[ 'The script had subjects with missing emails on ' date ' while sending out ' days ' day reminders for the ' calendar ' calendar. The attached mat file contains these subjects!'],'APPTS.mat');
	end
	end

	% Exit from matlab to run the next script
	exit

	end
	function send_brains()
	% SEND BRAIN IMAGES (send_brains.m)
	% Vanessa Sochat
	%
	% This script takes in a list of subjects processed in SPM, creates a brain
	% images zip with two .JPG images to send to the subject, and sends it.
	%__________________________________________________________________________
	%
	% DEPENDENCIES: You need to have the crop.m script in the same folder for
	% this to work: http://vsoch.com/LONG/Vanessa/MATLAB/Send%20Brains/crop.m
	%
	% SUBJECT ID: This script is set up to work with DNS data - it is expecting
	% IDs to have the format (DATE)_(SUBJECT ID). As the subject output images
	% are named with the five numbers after the "_" (representing the subject
	% ID) - this is the format that the script is expecting. If your subject
	% IDs do not fit this format, you can nix the section that goes through the
	% processed subject names and creates a string of modified IDs and just use
	% the processed subject list raw without any changes to compare the files
	% variable list to.
	%
	%__________________________________________________________________________
	%
	% USAGE: send_brains()
	% no input variables are required as the program takes them into a GUI.
	%__________________________________________________________________________
	%
	% ORGANIZATION: You should maintain the following file structure:
	% Output images under DNS.01\Graphics\Brain Images
	% Input Data: We will be using the processed highres under "anat"
	% sdns01-005-00001-000001-01.img, to create the image from.
	%__________________________________________________________________________
	%
	% This script works by....
	% 1. Creating the list of potential sendees - whoever has been newly
	% processed that week and does not have a brain image created yet.
	% 2. The script then presents this list to the user, and asks if he/she
	% would like to delete any participants. This is important because we
	% could have a test folder under Processed, or potentially a participant
	% that we don't want to send to. To delete a participant, the user simply
	% enters the ID into the GUI, and then the script presents the user with
	% the new list. There is no negative consequence of making a typo and
	% entering an incorrect ID - the script will not find the ID in the list,
	% and will present the identical list to the user, and he/she can enter
	% the ID again.
	% 3. Next, the script looks for the processed anatomical in the subject's
	% anat directory under Processed. This image will normally always have
	% the same name - however in rare cases when the name is different,
	% for whatever reason, the script will not find the highres, and will
	% present the user with a GUI to select the image that he/she would like
	% to use for that participant. It then prepares two slice views of the
	% highres, crops them, puts them together as a zip, moves the zip to the
	% Graphics/Brain Images folder, and cleans up the old files.
	% 4. Once all brain image zips have been created, the script prompts the
	% user if he/she wants to send a brain image for each subject, and asks
	% the user to enter the email. This process is fairly rapid and easy.
	% In the case that the user mistypes an email, the easiest thing to do
	% is delete the output image, and quickly run the script again.
	% 5. As each address in entered, the script sends the email directly from
	% MATLAB.
	%__________________________________________________________________________
	%__________________________________________________________________________


	%-Global Variables
	%-----------------------------------------------------------------------
	fprintf('SEND_BRAIN.M Alpha\n Vanessa Sochat\n August, 2010\n');

	% Here the user specifies the experiment directory
	homedir = spm_select(1,'dir','Select top of experiment directory','','N:');

	% Here the user specifies the output directory
	output = spm_select(1,'dir','Select output directory','',[ homedir 'Graphics\' ] );

	% Here we set the Processed directory
	processed_dir = horzcat(homedir,'Analysis\SPM\Processed\');

	% Add the path to the crop script
	addpath(genpath('N:\DNS.01\Scripts\MATLAB\Vanessa\Send Brains'));

	%-Identify subject list to make brain images for
	%-----------------------------------------------------------------------
	% Here the script compares the subjects in the "Processed" folder (meaning
	% they have been processed and we can send a brain image) to the brain
	% images in the output folder. The subject IDs that appear in the Processed
	% folder but not the output folder are saved into a variable as they need
	% to have brain images sent. Then, the user is allowed to delete subjects
	% or text from the string, as it could be likely that there is a TEST
	% folder or file in the processed directory that isn't a subject to send
	% brain images to.

	% First get the processed subjects
	cd(processed_dir)
	processed = [ ls ];

	% And then we grab the subject IDs who have had brain images.
	cd(output);
	files = [ ls ];

	% Initialize brain_list variables
	brain_list = '';

	% We start at the third element because the first two are "." and ".."
	for c = 3:size(processed,1)

	% The subject ID always starts at the 10th spot, and ends at te 15th, so we
	% use those coordinates to pull the subject IDs fromn the processed variable.
	% You will need to change this if you have a different format, or you could
	% just get rid of it completely and use the entire subject ID for the image names.
	current_processed = processed(c,:);


	% By default, add_var starts out as 'yes' and only gets changed to
	% no if we find a matched subject ID.
	add_var = 'yes';

	% VANESSA - MIGHT WANT TO ADD SOME SORT OF BREAK IF A MATCH IS
	% FOUND, SO DON'T KEEP SEARCHING ONCE IS FOUND!
	for i = 1:size(files,1)
	% We take the first 5 characters of the file name, which is the
	% subject's ID
	subject = files(i,1:5);

	if strcmp(current_processed(10:14),subject)
	% If the processed subject can be found under the output files
	% list, then the brain image has already been processed and we
	% exit the loop without adding anything
	add_var = 'no';
	end
	end

	% After cycling through the list of brain images already made, we only
	% flag the subject as needing an image if the add_var is set to "yes" -
	% meaning that no match was ever found.
	if strcmp(add_var,'yes')
	brain_list = [ brain_list;current_processed ];
	end

	% and now we move on to the next processed subject at the start of the
	% loop
	end

	% Clean up
	clear current_processed subject

	fprintf('%s\n','The list of subjects that need brain images is...');
	selections = listdlg('PromptString','Select Subjects to send to:','SelectionMode','multiple','ListString',brain_list);

	% Pull the user selections from the brain list, and put them in the
	% temp_list

	add_count = 0;
	for j = 1:size(selections,2)
	add_count = add_count +1;
	temp_list{add_count} = deblank(brain_list(selections(j),:));
	end

	clear selections

	%-Create brain images
	%-----------------------------------------------------------------------
	% This part of the script goes to the subject's anatomical directory,
	% creates the brain image, and saves it to the output directory.

	% Initialize graphic viewer
	spm_figure('GetWin','Graphics');
	clear global st

	% Read in logo and prepare file array (to make zip) just once!
	I = imread('http://www.haririlab.com/img/logo_small.jpg');
	I = imresize(I, 2);
	imagefiles{1}='slices.JPG';
	imagefiles{2}='sagittal.JPG';

	for i=1:size(temp_list,2)
	subject = temp_list{i};

	% CD to subject's anatomical folder
	if exist(horzcat(processed_dir,subject,'/anat/'),'dir')
	cd(horzcat(processed_dir,subject,'/anat/'));

	% If the default anatomical/highres exists, we use that
	if exist(horzcat(processed_dir,subject,'/anat/sdns01-0005-00001-000001-01.img'),'file');
	anat = horzcat(processed_dir,subject,'/anat/sdns01-0005-00001-000001-01.img');

	% Create slices view and save...
	SO=slover();
	SO.img(1).vol=spm_vol(anat);
	SO.slices = [-36:2:70];
	SO=paint(SO);

	% Add logo to slices image and save
	image(I)
	axis off
	print -dtiff -noui slices.JPG
	crop('slices.JPG');

	% Print sagittal view
	SO=slover();
	SO.img(1).vol=spm_vol(anat);
	SO.slices = [-2:10:52];
	SO.transform = 'sagittal';
	SO=paint(SO);
	axis off
	print -dtiff -noui sagittal.JPG
	crop('sagittal.JPG');

	% Prepare zip of two files
	zip('brain',imagefiles)

	% Save final image to output directory
	copyfile('brain.ZIP',[ output,subject(10:14),'.ZIP' ]);
	delete brain.ZIP
	delete slices.JPG
	delete sagittal.JPG
	clear SO
	else
	% If not, we give the user the option to select the file
	h = msgbox([ 'Default highres does not exist for ' subject '!' ],'File Not Found','warn');
	uiwait(h);

	files = [ ls ];

	[ selection use_anat ] = listdlg('PromptString','Select file, or CANCEL to skip','SelectionMode','single','ListString',files);

	if use_anat == 1

	anat = files(selection,:);

	% Create slices view and save...
	SO=slover();
	SO.img(1).vol=spm_vol(anat);
	SO.slices = [-36:2:70];
	SO=paint(SO);

	% Add logo to slices image and save
	image(I)
	axis off
	print -dtiff -noui slices.JPG
	crop('slices.JPG');

	% Print sagittal view
	SO=slover();
	SO.img(1).vol=spm_vol(anat);
	SO.slices = [-2:10:52];
	SO.transform = 'sagittal';
	SO=paint(SO);
	axis off
	print -dtiff -noui sagittal.JPG
	crop('sagittal.JPG');

	% Prepare zip of two files
	zip('brain',imagefiles)

	% Save final image to output directory
	copyfile('brain.ZIP',[ output,subject(10:14),'.ZIP' ]);
	delete brain.ZIP
	delete slices.JPG
	delete sagittal.JPG
	clear SO

	else
	fprintf('%s%s%s\n','Please take not that subject ',subject,' has been skipped!');
	end
	end
	else
	fprintf('%s%s%s\n','Subject ',subject,' does not have an anat folder under Processed!')
	end
	end

	%-Send Brain Images
	%-----------------------------------------------------------------------
	% This part of the script goes to the output directory and sends an email
	% for each subject
	cd(output);

	% Must be in the same folder as the script
	load poozie.mat

	% Then this code will set up the preferences properly:
	setpref('Internet','E_mail',poozie);
	setpref('Internet','SMTP_Server','smtp.gmail.com');
	setpref('Internet','SMTP_Username',poozie);
	setpref('Internet','SMTP_Password',pooziepa);
	props = java.lang.System.getProperties;
	props.setProperty('mail.smtp.auth','true');
	props.setProperty('mail.smtp.socketFactory.class', 'javax.net.ssl.SSLSocketFactory');
	props.setProperty('mail.smtp.socketFactory.port','465');

	for i=1:size(temp_list,2)
	subject = temp_list{i};
	send_var=spm_input([ 'Send image to:',subject(10:14),'?' ],1,'Yes\|No');
	if strcmp(send_var,'Yes')
	email = spm_input([ subject(10:14),' email address:' ],2,'s','',1);

	% Check to see if the brain image exists, just in case!
	if exist([ subject(10:14),'.ZIP' ],'file')
	brain_image=[ subject(10:14),'.ZIP' ];
	% Send the email. Note that the first input is the address!
	sendmail(email,'Laboratory of Neurogenetics - Brain Image','Attached, please find an image of your brain. This image is intended for personal use only. The image is NOT intended as and should NOT be used as a substitute for medical evaluation.',brain_image);
	else
	fprintf('%s%s/n',subject(10:14),'.ZIP cannot be found! Brain image not sent!');
	end
	end
	end

	fprintf('%s\n','Done sending brain images!');

	end