Merge branch 'develop'

+toppe/+utils/coppe.m

@@ -1,97 +1,130 @@
 function coppe(varargin)
 % function coppe(varargin)
-%  Function for **internal** University of Michigan fMRI lab use only to
-%  send toppe files automatically to our scanners. Can be generalized for
-%  other sites but the server names need to be updated.
-%
-%  A rough copy of the bash script called in this function (pushtoppefiles)
-%  that we have on lab servers that can access the scanner is the 
-%  following:
-%
-%       #!/bin/bash
-%       # Support file for copying toppe scan files to the scanner, then unpacking them
-%       set -e
-%       IP=$(getscannerip)
-%       echo "Copying files to scanner..."
-%       ssh sdc@$IP 'scp fmrilab@toro:~/toppe_utils/toppe-scanfiles.tgz /usr/g/bin/; cd /usr/g/bin/; tar -xzf toppe-scanfiles.tgz'
-%
+%   Function for **internal** University of Michigan fMRI lab use only to
+%   send toppe files automatically to our scanners. Can be generalized for
+%   other sites but the server names need to be updated.
 %
 % Input options:
-%  target   which scanner to copy pulse sequence to, UM options: 'inside', 'outside'
-%  use_pw   option to allow command line input, in the case a pw is needed
-%  cv       CV number, used to determing where on the scanner to put files
+%   cv      CV number, used to determing where on the scanner to put files
+%   target  which scanner to copy pulse sequence to, UM options: 'inside', 'outside'
+%   force   option to force overwrite of existing sequences corresponding
+%           to cv (default is 0, no overwrite)
+%   user    user name on server to use for file transfer (defaults to current user name)
+%   use_pw  option to allow command line input, in the case a pw is needed
+%           (default is 0)
+%   dir     target directory to write to under /srv/nfs/psd/usr/psd on scanner
+%           (default is [username]/toppe[cv #])
+%   version toppe software version (5 for tv5, 6 for tv6)
 %
 % Packages toppe files into toppe-scanfiles.tgz, then copies it to the scanner
-% Assumes you have SSH keys set up to log into romero/toro
-
-import toppe.utils.*
-
-arg.target = 'inside'; % Default to inside scanner
-arg.use_pw  = false;   % assume we have ssh keys setup to not need a pw
-arg.cv = [];           % if no CV given, it will coppe to /usr/g/bin
-arg = vararg_pair(arg, varargin);
+% Assumes you have the following SSH keys set up:
+%   1. ssh key from host --> server
+%   2. ssh key from scanner --> host
+%
+% if SSH keys require a passcode, set use_pw = 1 to show prompt
+%
 
-fprintf('Making archive...');
-[status,cmdout] = system('tar czf toppe-scanfiles.tgz modules.txt seqstamp.txt scanloop.txt *.mod'); fprintf('done!\n');
+    import toppe.utils.*
+    basedir = '/srv/nfs/psd/usr/psd'; % base directory on scanner
+
+    % Set default arguments
+    arg.target = 'inside';
+    arg.force = 0;
+    [~,arg.user] = system('echo -n $USER');
+    arg.use_pw  = 0;
+    arg.cv = [];
+    arg.dir = 'auto';
+    arg.version = 6; %Toppe version
+    arg = vararg_pair(arg, varargin);
 
-if status
-    error(cmdout)
-end
+    % set the default target directory
+    if strcmpi(arg.dir,'auto')
+        arg.dir = sprintf('%s/toppe%d', arg.user, arg.cv);
+    end
 
-% Create string for calling bash script on server
-if isempty(arg.cv)
-    script2call = 'pushtoppefiles';
-else
-    script2call = ['pushtoppefiles ', num2str(arg.cv)];
-end
+    % get the host IP address
+    [~,host_IP] = system('wget -qO- ifconfig.me/ip');
+
+    % zip the sequence using tar
+    fprintf('Zipping toppe files using tar...');
+    if(arg.version < 6)
+        [status,cmdout] = system('tar czf toppe-scanfiles.tgz modules.txt seqstamp.txt scanloop.txt *.mod');
+    else
+        [status,cmdout] = system('tar czf toppe-scanfiles.tgz modules.txt seqstamp.txt scanloop.txt cores.txt toppeN.entry *.mod');
+    end
+    if status
+        error(cmdout)
+    else
+        fprintf(' SUCCESS\n');
+    end
 
-try
     % set server names
     switch arg.target
         case 'inside'
-            server_str = 'romero';
-            homedir_str = '/export/home/fmrilab';
+            server_str = 'epyc';
         case 'outside'
-            server_str = 'toro';      
-            homedir_str = '/home/fmrilab';
+            server_str = 'goliath';
         otherwise
-            fprintf('Invalid target, valid targets are ''inside'' or ''outside''.\n');
+            error('Invalid target, valid targets are ''inside'' or ''outside''.\n');
     end
 
-    %% create linux commands with correct server target and run
-
-    cmd1 = ['scp toppe-scanfiles.tgz fmrilab@',server_str,':~/toppe_utils/'];
-    cmd2 = ['ssh -q fmrilab@',server_str,' ',homedir_str,'/toppe_utils/', script2call];
-
-    % 1. Send toppe files to server
-    fprintf(['Copying to ',server_str,'...']);
-    if ~arg.use_pw
-        [st1, cmdo1] = system(cmd1);
-    else
-        [st1, cmdo1] = system(cmd1,'-echo');
+    % Set up the commands to run on the scanner
+    cmd_scanner = [];
+    if ~arg.force
+        % check for existing entry file
+        cmd_scanner = sprintf('%s if [[ -f %s/pulseq/toppe%d.entry ]]; then exit 15; fi;', ...
+            cmd_scanner, basedir, arg.cv);
     end
-    if st1, error(cmdo1); end; fprintf('done!\n');
+    % check if directory exists, if it doesn't, create it
+    cmd_scanner = sprintf('%s if [ ! -d %s/%s ]; then mkdir -p %s/%s; fi;', ...
+            cmd_scanner, basedir, arg.dir, basedir, arg.dir);
+    % cd into the directory
+    cmd_scanner = sprintf('%s if ! cd %s/%s; then exit 16; fi;', ...
+        cmd_scanner, basedir, arg.dir);
+    % scp toppe files from host
+    cmd_scanner = sprintf('%s if ! scp -q %s@%s:%s/toppe-scanfiles.tgz ./; then exit 17; fi;', ...
+        cmd_scanner, arg.user, host_IP, pwd);
+    % unzip the tar file
+    cmd_scanner = sprintf('%s if ! tar -xzf toppe-scanfiles.tgz; then exit 18; fi; rm toppe-scanfiles.tgz;', ...
+        cmd_scanner);
+    % rename the entry file and move it to pulseq directory
+    cmd_scanner = sprintf('%s if ! mv toppeN.entry %s/pulseq/v%d/toppe%d.entry; then exit 19; fi;', ...
+        cmd_scanner, basedir, arg.version,arg.cv);
+    % replace the first line with the right directory
+    cmd_scanner = sprintf('%s if ! sed -i "1s#.*#%s/%s/#" %s/pulseq/v%d/toppe%d.entry; then exit 20; fi;', ...
+        cmd_scanner, basedir, arg.dir, basedir, arg.version, arg.cv);
+
+    % ssh into server, then into scanner, and run the scanner commands using bash
+    cmd_host = sprintf('ssh -q %s@%s ssh -q sdc@10.0.1.1 /bin/bash << EOF\n%s\nEOF', ...
+        arg.user, server_str, cmd_scanner);
 
-    % 2. Send toppe files from server to scanner computer and untar
-    fprintf('Copying to scanner and untaring ...');
-    if ~arg.use_pw
-        [st2, cmdo2] = system(cmd2);
+    % use -echo to show the bash output (in case pw is required)
+    if arg.use_pw
+        eval_args = {cmd_host, '-echo'};
     else
-        [st2, cmdo2] = system(cmd2,'-echo');
+        eval_args = {cmd_host};
     end
-    if st2, error(cmdo2); end; fprintf('done!\n');
-
-
-    %% Find minimum number of slices
-    disp('Files sucessfully copied. Finding # of slices...');
-    scanloop_struc = importdata('scanloop.txt');
-    scanloop_struc_data = scanloop_struc.data;
-    max_sli = scanloop_struc_data(2);
-    fprintf('Set # of slices on scanner to %d or greater.\n',max_sli+1);
-
-    disp('Ready to scan.');
-catch
-    fprintf('\n...failed. Not ready to scan.\n');
+
+    % Copy the file to the scanner and unzip
+    fprintf('Copying to scanner and unzipping...');
+    [out,msg] = system(eval_args{:});
+    switch out
+        case 15
+            error('cv number %d is already taken, use force argument to force overwrite', arg.cv);
+        case 16
+            error('failed to cd into %s/%s\noutput:\n%s', basedir, arg.dir, msg)
+        case 17
+            error('failed to scp from host to scanner, are your keys set up right?\noutput:\n%s', msg)
+        case 18
+            error('failed to unzip the tar file\noutput:\n%s', msg)
+        case 19
+            error('failed to move the entry file\noutput:\n%s', msg)
+        case 0
+            fprintf(' SUCCESS\nsequence files written to %s/%s\n', basedir, arg.dir);
+        otherwise
+            error('unknown error\noutput:\n%s',msg)
+    end
+
 end
 
 

+toppe/+utils/getk.m

@@ -0,0 +1,26 @@
+function [kxo, kxe] = getk(sysGE, readoutFile, nfid, del)
+% Get kspace sample locations from .mod file
+% 
+% Inputs:
+%  sysGE          see toppe.systemspecs()
+%  readoutFile    .mod file name containing ADC window
+%  nfid           number of acquired samples in ADC window
+%
+% Option:
+%  del            offset by this many samples (default: 0)
+%
+% Outputs:
+%  kxo            [1 nfid], odd echo k-space, cycles/cm
+%  kxe            [1 nfid], even echo k-space, cycles/cm
+
+if nargin < 4
+    del = 0.0;
+end
+
+[rf,gx,gy,gz,desc,paramsint16,paramsfloat,hdr] = toppe.readmod(readoutFile);
+kx = sysGE.raster*1e-6*sysGE.gamma*1e-4*cumsum(gx);  % cycles/cm
+kx = kx - kx(end)/2;
+kx = kx((hdr.npre+1):(hdr.npre+nfid));
+kxo = interp1(1:nfid, kx, (1:nfid) - 0.5 - del, 'linear', 'extrap');
+kxe = interp1(1:nfid, kx, (1:nfid) + 0.5 + del, 'linear', 'extrap');
+kxe = fliplr(kxe);

+toppe/plotseq.m

@@ -298,7 +298,6 @@
 
     p = loop(n,1);   % module id
     w = loop(n,16);  % waveform index
-
     dur = 0;
 
     % Pure delay block
@@ -330,7 +329,7 @@
 
     % Calculate RF and gradient waveforms for this block
     rho1 = [ia_rf/max_pg_iamp*abs(modules{p}.rf(:,w))];
-    th1 = [ia_rf/max_pg_iamp*angle(modules{p}.rf(:,w))];
+    th1 = angle(modules{p}.rf(:,w));
     gxit = ia_gx/max_pg_iamp*modules{p}.gx(:,w);
     gyit = ia_gy/max_pg_iamp*modules{p}.gy(:,w);
     gzit = ia_gz/max_pg_iamp*modules{p}.gz(:,w);

+toppe/preflightcheck.m

@@ -69,7 +69,7 @@ function preflightcheck(entryFile, seqstampFile, sysGE)
 modArr = toppe.tryread(@toppe.readmodulelistfile, moduleListFile);
 
 % Check that:
-%  - all .mod files use the same peak RF limit (e.g., 0.25 Gauss)
+%  - b1CheckFile represents the RF pulse with peak RF amplitude across the whole the sequence
 %  - all .mod files used to acquire data have the same number of ADC samples as readoutFilterFile.
 [~,~,~,~,~,~,~,hdr] = toppe.readmod(b1CheckFile);
 b1limit = hdr.b1max;
@@ -82,8 +82,8 @@ function preflightcheck(entryFile, seqstampFile, sysGE)
         error(sprintf('Number of samples in %s and %s do not match (must be same across all .mod files containing ADC windows)', ...
             readoutFilterFile, modArr{ii}.fname));
     end
-    if hdr.b1max ~= b1limit 
-        error(sprintf('B1 limit in %s does not match %s (must be the same across all .mod files)', ...
+    if modArr{ii}.hasRF & hdr.b1max > b1limit 
+        error(sprintf('Peak B1 limit in %s cannot exceed the b1 scaling .mod file in %s', ...
             modArr{ii}.fname, entryFile));
     end
 end
@@ -196,7 +196,7 @@ function preflightcheck(entryFile, seqstampFile, sysGE)
 fprintf(fout, '%.4f\n', max(abs(rf)));  % needed to scale max_seqsar in .e file
 fprintf(fout, '%.4f\n', gmax);          % max gradient across all .mod files (Gauss)
 fprintf(fout, '%.4f\n', slewmax);       % max slew across all .mod files (G/cm/ms)
-fprintf(fout, '%.4f\n', b1limit);       % hardware b1 limit (Gauss) 
+fprintf(fout, '%.4f\n', b1limit);       % peak B1 in sequence (Gauss)
 
 fclose(fout);
 

+toppe/systemspecs.m

@@ -27,7 +27,7 @@
 % Design choices (need not equal scanner limits)
 sys.maxGrad  = 4;      % Gauss/cm
 sys.maxSlew  = 15;     % Gauss/cm/ms
-sys.maxRF    = 0.25; 
+sys.maxRF    = 0.15; 
 sys.rfDeadTime = 72;         % us. Must be >= 72us
 sys.rfRingdownTime = 54;     % us. Must be >= 54us
 sys.adcDeadTime = 40;        % us. Must be >= 40us

+toppe/writemod.m

@@ -144,7 +144,8 @@ function writemod(sysGE, varargin)
 dtycyc        = length(find(abs(b1)>0.2236*max(abs(b1)))) / length(b1);
 maxpw         = dtycyc;
 num           = 1;
-max_b1        = sysGE.maxRF;                       	% Gauss. Full instruction amplitude (32766) should produce max_b1 RF amplitude,
+max_b1        = sysGE.maxRF;        % Gauss. Full instruction amplitude (32766) should produce max_b1 RF amplitude,
+%max_b1        = max(abs(b1(:)));     % Gauss
 																		% as long as other RF .mod files (if any) use the same max_b1.
 max_int_b1_sq = max( cumsum(abs(b1).^2)*dt*1e3 );   	% Gauss^2 - ms
 max_rms_b1    = sqrt(mean(abs(b1).^2));              	% Gauss