int main(int argc, char const *argv[])
{
link *head = NULL;
link *curr = NULL;
int guests,time,value,i;
printf("enter the number of guests\n");
scanf("%d",&guests);
int array[2*guests];
for (i = 0; i < 2*guests; ++i)
{
if (i<guests)
value = 1;
else
value = -1;
scanf("%d",&time);
insert(&head,&curr,time,value);
}
int times[2*guests];
int values[2*guests];
gettimevalues(head,times,values);
sortarrays(times,values,2*guests);
for (i = 0; i < 2*guests; ++i)
printf("%d \t",times[i]);
printf("\n");
for (i = 0; i < 2*guests; ++i)
printf("%d",values[i]);
changevalues(&head,&curr,times,values);
for ( i= 0; i < 2*guests; ++i)
array[i] = 0;
getarray(&head,&curr,array);
printf("\n");
for ( i = 0; i < 2*guests; ++i)
printf("%d\t",array[i]);
printf("\n\n%d",getmax(array,2*guests));
return 0;
}
int main(void) {
int *a; int n;
int r; int random;
int d;
scanf("%d", &n); a = getarray(n);
scanf("%d", &random); // Randomizer
scanf("%d", &r); // Elements are 0 - r
fill(random, r, n, a);
arrayprint(n, a);
scanf("%d", &d); // Looking for d
lin_search(d, n, a);
insertion_sort(n, a);
arrayprint(n, a);
lin_search(d, n, a);
bin_search(d, n, a);
return 0;
}
/*-----------------------------------------------*/
void getparsRf(RF_PULSE_T *rf)
{
int i;
char parname[MAX_STR];
/* Initialise pars */
for (i=0;i<MAXRFPARS;i++) rf->pars[i]=0.0;
/* Generate "*pars" name from the base name */
strcpy(parname,rf->pulseBase);
strcat(parname,"pars");
/* This will report a suitable error if the "*pars" parameter does not exist */
rf->npars=(int)getarray(parname,rf->pars);
/* Current "*pars" definition is that it contains the following elements:
pulse resolution in usec
pulse bandwidth in Hz
number of lobes
amplitude cutoff as a % of maximum
HS mu
HS beta in rad/s
modulation frequency in Hz
*/
/* There must be at least one value */
rf->res = rf->pars[0];
/* Now get the rest */
if (rf->npars > 1) rf->bandwidth = rf->pars[1];
if (rf->npars > 2) rf->lobes = (int)sglRoundPositive(rf->pars[2]);
if (rf->npars > 3) rf->cutoff = rf->pars[3];
if (rf->npars > 4) rf->mu = rf->pars[4];
if (rf->npars > 5) rf->beta = rf->pars[5];
if (rf->npars > 6) rf->modfrq = rf->pars[6];
}
void eval(char* s, int pipes)
{
pid_t* pids = malloc(sizeof(pid_t*)*(pipes+1));
if (!pipes) pids[0] = run(s,0,1);
else
{
char** programs = getarray(s,"|");
if (programs == NULL) return;
int* oldpipes = NULL;
int* newpipes = NULL;
for (int i = 0; i <= pipes; i++)
{
newpipes = malloc(sizeof(int)*2);
if (newpipes == NULL)
{
perror("ish malloc newpipes");
return;
}
int p = pipe(newpipes);
if (p < 0)
{
perror("ish pipe");
return;
}
if (programs[i+1] == NULL) newpipes[1] = 1;
if (oldpipes == NULL) pids[i] = run(programs[i],0,newpipes[1]);
else pids[i] = run(programs[i],oldpipes[0],newpipes[1]);
free(oldpipes);
oldpipes = newpipes;
}
}
// Allow everything to finish up
for (int i = 0; i <= pipes; i++)
{
waitpid(pids[i],NULL,0);
}
}
int main(int argc, char *argv[]) {
int nelem, nimages;
float *tagon[MAXELEM], *tagoff[MAXELEM], *tagdiff[MAXELEM]; // Images
double *tagctrl; // tag control variable values
float *mean_on, *mean_off, // mean of tag on/off images
*mean_diff, // mean of pairwise difference images
*diff_mean; // difference of mean on/off images
double *image_arr;
fdf_header fdf_hdr;
char filename[MAXSTR];
float noise_thr = 0;
// Loop variables
int slice, image, images, ndiff;
int pixel, datapts;
int i;
int debug_pixel, debug;
/* input arguments */
user_input input = {
0, // debug
"asltag", // tagvar
-1, // noise
-1, // pixel
"ASL", // outdir
".", // indir
0, // write all pairs of subtracted images
0, // subtraction scheme (integer), default strict pairs
"pair" // subtraction scheme (string), default strict pairs
};
/*******************************************************************/
/*** Calculations **************************************************/
/*******************************************************************/
// Get arguments from commandline
get_args(&input, argc, argv);
debug = input.debug;
if (debug) {
if (input.pixel < 0)
debug_pixel = fdf_hdr.ro_size/2*fdf_hdr.pe_size + fdf_hdr.pe_size/2;
else
debug_pixel = input.pixel;
}
else debug_pixel = -1;
/* Set up string for procpar;
this is for future expansion, to allow
- data to be in arbitrary directory
- S(0) and S(non-zero)to be in different directories
*/
strcpy(procpar,input.indir);
strcat(procpar,"/procpar");
if (debug) printf("indir = %s, procpar = %s\n",input.indir,procpar);
// Determine the number of images
nelem = getstatus(input.tagvar);
if (nelem == 0) {
exit(0); // error message is printed by getstatus
}
// Read tag control variable
if ((tagctrl = (double *) malloc(sizeof(double)*nelem)) == NULL) nomem();
getarray(input.tagvar,tagctrl);
/* Is this an epi scan with reference scan(s)? */
images = getstatus("image");
if (images == nelem) { // assume image is arrayed in parallel with the variable
//find out how many ref scans
if ((image_arr = (double *) malloc(sizeof(double)*images)) == NULL) nomem();
getarray("image",image_arr);
nimages = 0;
for (i = 0; i < images; i++)
if (image_arr[i] == 1)
nimages++;
}
else nimages = nelem;
if (debug) printf("nelem, nimages, images = %d, %d, %d\n",nelem, nimages, images);
/* XXX Check if we have an equal number of tag on/off ??? */
/* Initialize fdf header */
init_fdf_header(&fdf_hdr);
/* Allocate memory for all images */
datapts = fdf_hdr.ro_size*fdf_hdr.pe_size;
switch(input.subtr) {
case 0: ndiff = nimages/2; break; //strict pairwise
case 1: ndiff = nimages - 1; break; // adjacent pairs
case 2: ndiff = nimages - 2; break; // "surround" subtraction
default: printf("Invalid subtraction scheme\n");exit(0);
}
for (image = 0; image < ndiff; image++) {
/* XXX CHECK if tagctrl = -1, 0 , 1 */
if ((tagon[image] = (float *)malloc(datapts*sizeof(float))) == NULL) nomem();
if ((tagoff[image] = (float *)malloc(datapts*sizeof(float))) == NULL) nomem();
if ((tagdiff[image] = (float *)malloc(datapts*sizeof(float))) == NULL) nomem();
}
if ((mean_on = (float *)malloc(datapts*sizeof(float))) == NULL) nomem();
if ((mean_off = (float *)malloc(datapts*sizeof(float))) == NULL) nomem();
if ((mean_diff = (float *)malloc(datapts*sizeof(float))) == NULL) nomem();
if ((diff_mean = (float *)malloc(datapts*sizeof(float))) == NULL) nomem();
/* Create directory to put output in */
if (strcmp(input.outdir, "./")) {
if (debug) printf("Making directory %s\n",input.outdir);
mkdir(input.outdir,0777);
}
/*******************************************************************/
/*** Slice by slice calculations ***********************************/
/*******************************************************************/
for (slice = 0; slice < fdf_hdr.slices; slice++) {
i = 0;
for (image = 0; image < nimages; image+=2) {
/* XXX check control variable */
/* Read tag on */
sprintf(filename,"%s/slice%03dimage%03decho001.fdf",
input.indir,slice+1,image+1);
if (debug) printf("tag on [%d]: %s\n",i,filename);
read_fdf_data(filename,tagon[i],&fdf_hdr);
/* Read tag off */
sprintf(filename,"%s/slice%03dimage%03decho001.fdf",
input.indir,slice+1,image+2);
if (debug) printf("tag off [%d]: %s\n",i,filename);
read_fdf_data(filename,tagoff[i],&fdf_hdr);
i++;
} // end read image loop
if (debug) printf("\n");
// Noise threshold - user input or based on histogram
if (input.noise > 0) noise_thr = input.noise;
else // Get noise from the first image
noise_thr = threshold(tagon[0],&fdf_hdr);
if (debug) printf("noise level %f\n",noise_thr);
/*******************************************************************/
/*** Pixel loop ****************************************************/
/*******************************************************************/
for (pixel = 0; pixel < datapts; pixel++) {
mean_diff[pixel] = 0;
if (tagon[0][pixel] > noise_thr) {
switch (input.subtr) {
case 0: // strictly pairwise: 0-0, 1-1, 2-2, ...
for (image = 0; image < nimages/2; image++) {
tagdiff[image][pixel] = (tagon[image][pixel] - tagoff[image][pixel]);
mean_diff[pixel] += tagdiff[image][pixel];
}
break;
case 1: // adjacent pairs: 0-0, 1-0, 1-1, 2-1, ...
i = 0;
for (image = 0; image < nimages/2-1; image++) {
tagdiff[i][pixel] = (tagon[image][pixel] - tagoff[image][pixel]);
mean_diff[pixel] += tagdiff[i][pixel];
i++;
if (pixel == debug_pixel) printf("subtract %d - %d\n",image,image);
tagdiff[i][pixel] = (tagon[image+1][pixel] - tagoff[image][pixel]);
mean_diff[pixel] += tagdiff[i][pixel];
if (pixel == debug_pixel) printf("subtract %d - %d\n",image+1,image);
i++;
}
tagdiff[i][pixel] = (tagon[nimages/2-1][pixel] - tagoff[nimages/2-1][pixel]);
if (pixel == debug_pixel) printf("subtract %d - %d\n",nimages/2,nimages/2);
mean_diff[pixel] += tagdiff[i][pixel];
break;
case 2: // surrounding pairs
i = 0;
for (image = 0; image < nimages/2-1; image++) {
tagdiff[i][pixel] = ((tagon[image][pixel]+tagon[image+1][pixel])/2 - tagoff[image][pixel]);
mean_diff[pixel] += tagdiff[i][pixel];
i++;
if (pixel == debug_pixel) printf("subtract %d+%d - %d\n",image,image+1,image);
tagdiff[i][pixel] = (tagon[image+1][pixel] - (tagoff[image][pixel]+tagoff[image+1][pixel])/2);
mean_diff[pixel] += tagdiff[i][pixel];
i++;
if (pixel == debug_pixel) printf("subtract %d - %d+%d\n",image+1,image,image+1);
}
break;
}
// divide by # pairs of images
mean_diff[pixel] /= ndiff;
} // end check noise threshold
} // end pixel loop
/* Write Images maps: */
fdf_hdr.array_dim = 1 + input.write_all*ndiff;
fdf_hdr.slice_no = slice + 1;
fdf_hdr.array_index = 1;
fdf_hdr.display_order = 1;
if (input.write_all) {
for (image = 0; image < ndiff; image++) {
// write tag difference image
sprintf(filename,"%s/tagdiff_%03d_%03d.fdf",input.outdir,image+1,slice+1);
write_fdf(filename,tagdiff[image],&fdf_hdr);
fdf_hdr.array_index++;
fdf_hdr.display_order++;
}
}
sprintf(filename,"%s/diff_%s_%03d.fdf",input.outdir,input.method,slice+1);
write_fdf(filename,mean_diff,&fdf_hdr);
fdf_hdr.array_index++;
fdf_hdr.display_order++;
} // end slice loop
}
pulsesequence()
{
/* Internal variable declarations *************************/
double freq90[MAXNSLICE],freq180[MAXNSLICE],freqIR[MAXNSLICE];
int shape90=0, shape180=0, shapeIR=0;
double te_delay1, te_delay2, tr_delay, ti_delay = 0;
double del1=0, del2=0, del3=0, del4=0;
double tau1=0, tau2=0, difftime=0, tetime=0;
int table=0;
/* Diffusion parameters */
#define MAXDIR 1024 /* Will anybody do more than 1024 directions or b-values? */
double roarr[MAXDIR], pearr[MAXDIR], slarr[MAXDIR];
int nbval, /* Total number of bvalues*directions */
nbro, nbpe, nbsl,
i;
double bro[MAXDIR], bpe[MAXDIR], bsl[MAXDIR], /* b-values along RO, PE, SL */
brs[MAXDIR], brp[MAXDIR], bsp[MAXDIR], /* and the cross-terms */
btrace[MAXDIR], /* and the trace */
max_bval=0,
dcrush, dgss2, /* "delta" for crusher and gss2 gradients */
Dro, Dcrush, Dgss2; /* "DELTA" for readout, crusher and gss2 gradients */
/* Real-time variables ************************************/
int vpe_steps = v1;
int vpe_ctr = v2;
int vms_slices = v3;
int vms_ctr = v4;
int vpe_offset = v5;
int vpe_index = v6;
int vph180 = v7; // Phase of 180 pulse
int vph2 = v8; // alternate phase of 180 on odd transients
/* Initialize paramaters *********************************/
init_mri();
/* Check for external PE table ***************************/
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
table = 1;
}
if ((diff[0] == 'y') && (gcrush < 4))
warn_message("Advisory: set gcrush to higher value to avoid image artifacts");
/* Initialize gradient structures *************************/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
init_rf(&p2_rf,p2pat,p2,flip2,rof2,rof2);
init_slice(&ss_grad,"ss",thk);
init_slice_butterfly(&ss2_grad,"ss2",thk*1.1,gcrush,tcrush);
init_slice_refocus(&ssr_grad,"ssr");
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
init_readout_refocus(&ror_grad,"ror");
init_phase(&pe_grad,"pe",lpe,nv);
/* RF Calculations ****************************************/
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
if (p2_rf.header.rfFraction != 0.5)
abort_message("RF pulse for refocusing (%s) must be symmetric",p2pat);
/* Gradient calculations **********************************/
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice(&ss2_grad,&p2_rf,WRITE,"gss2");
calc_slice_refocus(&ssr_grad, &ss_grad, NOWRITE,"gssr");
calc_readout(&ro_grad, WRITE, "gro","sw","at");
ro_grad.m0ref *= grof;
calc_readout_refocus(&ror_grad, &ro_grad, NOWRITE, "gror");
calc_phase(&pe_grad, NOWRITE, "gpe","tpe");
/* Equalize refocus and PE gradient durations *************/
calc_sim_gradient(&ror_grad, &pe_grad, &ssr_grad,0,WRITE);
/* Set up diffusion gradient */
if (diff[0] == 'y') {
init_generic(&diff_grad,"diff",gdiff,tdelta);
calc_generic(&diff_grad,NOWRITE,"","");
/* adjust duration, so tdelta is from start ramp up to start ramp down */
if (ix == 1) diff_grad.duration += diff_grad.tramp;
calc_generic(&diff_grad,WRITE,"","");
}
/* Min TE *************************************************/
tau1 = ss_grad.rfCenterBack + pe_grad.duration + 4e-6 + ss2_grad.rfCenterFront;
tau2 = ss2_grad.rfCenterBack + ror_grad.duration + ro_grad.timeToEcho + alfa;
temin = 2*(MAX(tau1,tau2) + 2*4e-6); /* have at least 4us between gradient events */
/* Calculate te_delays with the current TE, then later see how diffusion fits */
if ((minte[0] == 'y') || (te < temin)) {
te_delay1 = temin/2 - tau1;
te_delay2 = temin/2 - tau2;
}
else {
te_delay1 = te/2 - tau1;
te_delay2 = te/2 - tau2;
}
if (diff[0] =='y') {
/* Is tDELTA long enough for RF refocusing gradient? */
if (tDELTA < diff_grad.duration + ss2_grad.duration)
abort_message("DELTA too short, increase to %.2fms",
(diff_grad.duration + ss2_grad.duration)*1000+0.005);
/* Is tDELTA too long for TE dead time? */
difftime = tDELTA + diff_grad.duration; // tDELTA + front & back half diff_grad
tetime = ss2_grad.duration + te_delay1 + te_delay2;
if (difftime > tetime) {
temin += (difftime - tetime);
}
}
/* We now know the minimum TE incl. diffusion */
if (minte[0] == 'y') {
te = temin;
putvalue("te",ceil(te*1e6)*1e-6); /* round up to nearest us */
}
if (te < temin) {
if (diff[0] == 'n') {
abort_message("TE too short. Minimum TE = %.2fms\n",temin*1000);
}
else {
abort_message("TE too short, increase to %.2fms or reduce DELTA to %.2fms",
temin*1000,(tetime-diff_grad.duration)*1000);
}
}
te_delay1 = te/2 - tau1;
te_delay2 = te/2 - tau2;
/* Set up delays around diffusion gradients */
/* RF1 - del1 - diff - del2 - RF2 - del3 - diff - del4 - ACQ */
if (diff[0] == 'y') {
del1 = (tetime - difftime)/2;
del4 = del1;
del2 = te_delay1 - diff_grad.duration;
del3 = te_delay2 - diff_grad.duration;
if (del3 < 0.0) { // shift diff block to right
del1 += del3;
del2 -= del3;
del4 -= del3;
del3 = 0;
} else if (del2 < 0.0) { // shift diff block to left
del1 -= del2;
del3 -= del2;
del4 += del2;
del2 = 0;
}
}
else { /* No diffusion */
del1 = 0;
del3 = 0;
del2 = te_delay1;
del4 = te_delay2;
}
/* Min TR *************************************************/
trmin = (ss_grad.duration - ss_grad.rfCenterBack) + te + ro_grad.timeFromEcho;
if (navigator[0] == 'y')
trmin += (pe_grad.duration + ro_grad.duration);
/* Optional prepulse calculations *************************/
if (sat[0] == 'y') {
create_satbands();
trmin += satTime;
}
if (fsat[0] == 'y') {
create_fatsat();
trmin += fsatTime;
}
if (mt[0] == 'y') {
create_mtc();
trmin += mtTime;
}
if (ir[0] == 'y') {
init_rf(&ir_rf,pipat,pi,flipir,rof2,rof2);
calc_rf(&ir_rf,"tpwri","tpwrif");
init_slice_butterfly(&ssi_grad,"ssi",thk,gcrushir,tcrushir);
calc_slice(&ssi_grad,&ir_rf,WRITE,"gssi");
tau1 = ss_grad.duration - ss_grad.rfCenterBack; /* duration of ss_grad before RF center */
ti_delay = ti - (ssi_grad.rfCenterBack + tau1);
if (ti_delay < 0) {
abort_message("TI too short, Minimum TI = %.2fms\n",(ti-ti_delay)*1000);
}
irTime = ti + ssi_grad.duration - ssi_grad.rfCenterBack; /* time to add to TR */
trmin += irTime;
trmin -= tau1; /* but subtract out ss_grad which was already included in TR */
}
trmin *= ns;
if (mintr[0] == 'y'){
tr = trmin + ns*4e-6;
putvalue("tr",tr);
}
if (tr < trmin) {
abort_message("TR too short. Minimum TR= %.2fms\n",trmin*1000);
}
tr_delay = (tr - trmin)/ns > 4e-6 ? (tr - trmin)/ns : 4e-6;
/***************************************************/
/* CALCULATE B VALUES ******************************/
if (diff[0] == 'y') {
/* Get multiplication factors and make sure they have same # elements */
/* All this is only necessary because putCmd only work for ix==1 */
nbro = (int) getarray("dro",roarr); nbval = nbro;
nbpe = (int) getarray("dpe",pearr); if (nbpe > nbval) nbval = nbpe;
nbsl = (int) getarray("dsl",slarr); if (nbsl > nbval) nbval = nbsl;
if ((nbro != nbval) && (nbro != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (readout)",seqfil);
if ((nbpe != nbval) && (nbpe != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (phase)",seqfil);
if ((nbsl != nbval) && (nbsl != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (slice)",seqfil);
if (nbro == 1) for (i = 1; i < nbval; i++) roarr[i] = roarr[0];
if (nbpe == 1) for (i = 1; i < nbval; i++) pearr[i] = pearr[0];
if (nbsl == 1) for (i = 1; i < nbval; i++) slarr[i] = slarr[0];
}
else {
nbval = 1;
roarr[0] = 0;
pearr[0] = 0;
slarr[0] = 0;
}
for (i = 0; i < nbval; i++) {
/* Readout */
Dro = ror_grad.duration;
bro[i] = bval(gdiff*roarr[i],tdelta,tDELTA);
bro[i] += bval(ro_grad.amp,ro_grad.timeToEcho,Dro);
/* Slice */
dgss2 = Dgss2 = ss_grad.rfCenterFront;
dcrush = tcrush; //"delta" for crusher part of butterfly
Dcrush = dcrush + ss_grad.rfDuration; //"DELTA" for crusher
bsl[i] = bval(gdiff*slarr[i],tdelta,tDELTA);
bsl[i] += bval(gcrush,dcrush,Dcrush);
bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval_nested(gcrush,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2);
/* Phase */
bpe[i] = bval(gdiff*pearr[i],tdelta,tDELTA);
/* Readout/Slice Cross-terms */
brs[i] = bval2(gdiff*roarr[i],gdiff*slarr[i],tdelta,tDELTA);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
/* Readout/Phase Cross-terms */
brp[i] = bval2(gdiff*roarr[i],gdiff*pearr[i],tdelta,tDELTA);
/* Slice/Phase Cross-terms */
bsp[i] = bval2(gdiff*slarr[i],gdiff*pearr[i],tdelta,tDELTA);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
btrace[i] = (bro[i]+bsl[i]+bpe[i]);
if (max_bval < btrace[i]) {
max_bval = (bro[i]+bsl[i]+bpe[i]);
}
} /* End for-all-directions */
putarray("bvalrr",bro,nbval);
putarray("bvalpp",bpe,nbval);
putarray("bvalss",bsl,nbval);
putarray("bvalrp",brp,nbval);
putarray("bvalrs",brs,nbval);
putarray("bvalsp",bsp,nbval);
putarray("bvalue",btrace,nbval);
putvalue("max_bval",max_bval);
/* Generate phase-ramped pulses: 90, 180, and IR */
offsetlist(pss,ss_grad.ssamp,0,freq90,ns,seqcon[1]);
shape90 = shapelist(p1pat,ss_grad.rfDuration,freq90,ns,0,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shape180 = shapelist(p2pat,ss2_grad.rfDuration,freq180,ns,0,seqcon[1]);
if (ir[0] == 'y') {
offsetlist(pss,ssi_grad.ssamp,0,freqIR,ns,seqcon[1]);
shapeIR = shapelist(pipat,ssi_grad.rfDuration,freqIR,ns,0,seqcon[1]);
}
/* Set pe_steps for profile or full image **********/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&null_grad);
initval(pe_steps/2.0,vpe_offset);
sgl_error_check(sglerror);
/* Return parameters to VnmrJ */
putvalue("rgss",ss_grad.tramp); //90 slice ramp
if (ss2_grad.enableButterfly) { //180 slice ramps
putvalue("rcrush",ss2_grad.crusher1RampToCrusherDuration);
putvalue("rgss2",ss2_grad.crusher1RampToSsDuration);
}
else {
putvalue("rgss2",ss2_grad.tramp);
}
if (ro_grad.enableButterfly) {
putvalue("rgro",ro_grad.crusher1RampToSsDuration);
}
else {
putvalue("rgro",ro_grad.tramp); //RO ramp
}
putvalue("tror",ror_grad.duration); //ROR duration
putvalue("rgror",ror_grad.tramp); //ROR ramp
putvalue("gpe",pe_grad.peamp); //PE max amp
putvalue("gss",ss_grad.ssamp);
putvalue("gro",ro_grad.roamp);
g_setExpTime(tr*(nt*pe_steps*arraydim + ssc));
/* PULSE SEQUENCE *************************************/
rotate();
obsoffset(resto);
roff = -poffset(pro,ro_grad.roamp);
delay(4e-6);
/* Begin phase-encode loop ****************************/
peloop(seqcon[2],pe_steps,vpe_steps,vpe_ctr);
/* Read external kspace table if set ******************/
if (table)
getelem(t1,vpe_ctr,vpe_index);
else
sub(vpe_ctr,vpe_offset,vpe_index);
settable(t2,2,ph180); // initialize phase tables and variables
getelem(t2,vpe_ctr,vph180);
add(oph,vph180,vph180); // 180 deg pulse phase alternates +/- 90 from receiver
mod2(ct,vph2);
dbl(vph2,vph2);
add(vph180,vph2,vph180); // Alternate phase for 180 on odd transients
/* Begin multislice loop ******************************/
msloop(seqcon[1],ns,vms_slices,vms_ctr);
if (ticks) {
xgate(ticks);
grad_advance(gpropdelay);
}
/* TTL scope trigger **********************************/
sp1on(); delay(5e-6); sp1off();
/* Prepulses ******************************************/
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
/* Optional IR pulse **********************************/
if (ir[0] == 'y') {
obspower(ir_rf.powerCoarse);
obspwrf(ir_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ssi_grad.name,ssi_grad.duration,0,0,ssi_grad.amp,NOWAIT);
delay(ssi_grad.rfDelayFront);
shapedpulselist(shapeIR,ssi_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ssi_grad.rfDelayBack);
delay(ti_delay);
}
/* Slice select RF pulse ******************************/
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shape90,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Phase encode, refocus, and dephase gradient ********/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,-ssr_grad.amp,
pe_grad.increment,vpe_index,WAIT);
delay(del1); // delay to start of first diffusion gradient
if (diff[0] == 'y') {
obl_shapedgradient(diff_grad.name,diff_grad.duration,
diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
}
delay(del2); // delay from end of diffusion to slice refocusing
/* Refocusing RF pulse ********************************/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shape180,ss2_grad.rfDuration,vph180,rof2,rof2,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
delay(del3); // delay from slice refocusing to second diffusion gradient
if (diff[0] == 'y') {
obl_shapedgradient(diff_grad.name,diff_grad.duration,
diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
}
delay(del4); // delay from end of diffusion gradient to readout event
/* Readout gradient and acquisition ********************/
roff = -poffset(pro,ro_grad.roamp);
obl_shapedgradient(ror_grad.name,ror_grad.duration,-ror_grad.amp,0,0,WAIT);
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
/* Rewind Phase encoding ******************************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,
pe_grad.increment,vpe_index,WAIT);
if (navigator[0] == 'y') {
roff = -poffset(pro,-ro_grad.roamp);
obl_shapedgradient(ro_grad.name,ro_grad.duration,-ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
}
/* Relaxation delay ***********************************/
delay(tr_delay);
endmsloop(seqcon[1],vms_ctr);
endpeloop(seqcon[2],vpe_ctr);
}
pulsesequence()
{
/* DECLARE AND LOAD VARIABLES */
void makeHHdec(), makeCdec(); /* utility functions */
char f1180[MAXSTR], /* Flag to start t1 @ halfdwell */
mag_flg[MAXSTR], /* magic-angle coherence transfer gradients */
C13refoc[MAXSTR], /* C13 sech/tanh pulse in middle of t1*/
NH2only[MAXSTR], /* spectrum of only NH2 groups */
T1[MAXSTR], /* insert T1 relaxation delay */
T1rho[MAXSTR], /* insert T1rho relaxation delay */
T2[MAXSTR], /* insert T2 relaxation delay */
TROSY[MAXSTR], /* do TROSY on N15 and H1 */
Hdecflg[MAXSTR], /* HH-h**o decoupling flag */
Cdecflg[MAXSTR]; /* low power C-13 decoupling flag */
int icosel, /* used to get n and p type */
ihh=1, /* used in HH decouling to improve water suppression */
t1_counter, /* used for states tppi in t1 */
rTnum, /* number of relaxation times, relaxT */
rTcounter; /* to obtain maximum relaxT, ie relaxTmax */
double tau1, /* t1 delay */
lambda = 0.91/(4.0*getval("JNH")), /* 1/4J H1 evolution delay */
tNH = 1.0/(4.0*getval("JNH")), /* 1/4J N15 evolution delay */
relaxT = getval("relaxT"), /* total relaxation time */
rTarray[1000], /* to obtain maximum relaxT, ie relaxTmax */
maxrelaxT = getval("maxrelaxT"), /* maximum relaxT in all exps */
ncyc, /* number of pulsed cycles in relaxT */
pwr_dly, /* power delay */
/* the sech/tanh pulse is automatically calculated by the macro "proteincal", */
/* and is called directly from your shapelib. */
pwClvl = getval("pwClvl"), /* coarse power for C13 pulse */
pwC = getval("pwC"), /* C13 90 degree pulse length at pwClvl */
rf0, /* maximum fine power when using pwC pulses */
rfst, /* fine power for the stCall pulse */
compH = getval("compH"), /* adjustment for H1 amplifier compression */
compN = getval("compN"), /* adjustment for N15 amplifier compression */
compC = getval("compC"), /* adjustment for C13 amplifier compression */
calH = getval("calH"), /* multiplier on a pw pulse for H1 calibration */
tpwrsf = getval("tpwrsf"), /* fine power adustment for soft pulse */
pwHs = getval("pwHs"), /* H1 90 degree pulse length at tpwrs */
pwHH = 0.0, /* pwHH = pwHs for HH h**o-decoupling */
tpwrs, /* power for the pwHs ("H2Osinc") pulse */
pwNlvl = getval("pwNlvl"), /* power for N15 pulses */
pwN = getval("pwN"), /* N15 90 degree pulse length at pwNlvl */
calN = getval("calN"), /* multiplier on a pwN pulse for calibration */
slNlvl, /* power for N15 spin lock */
slNrf = 1500.0, /* RF field in Hz for N15 spin lock at 600 MHz */
sw1 = getval("sw1"),
gt1 = getval("gt1"), /* coherence pathway gradients */
gzcal = getval("gzcal"), /* dac to G/cm conversion */
gzlvl1 = getval("gzlvl1"),
gzlvl2 = getval("gzlvl2"),
BPpwrlimits, /* =0 for no limit, =1 for limit */
gt0 = getval("gt0"), /* other gradients */
gt3 = getval("gt3"),
gt4 = getval("gt4"),
gt5 = getval("gt5"),
gstab = getval("gstab"),
gzlvl0 = getval("gzlvl0"),
gzlvl3 = getval("gzlvl3"),
gzlvl4 = getval("gzlvl4"),
gzlvl5 = getval("gzlvl5");
P_getreal(GLOBAL,"BPpwrlimits",&BPpwrlimits,1);
getstr("f1180",f1180);
getstr("mag_flg",mag_flg);
getstr("C13refoc",C13refoc);
getstr("NH2only",NH2only);
getstr("T1",T1);
getstr("T1rho",T1rho);
getstr("T2",T2);
getstr("TROSY",TROSY);
getstr("Hdecflg", Hdecflg);
getstr("Cdecflg", Cdecflg);
/* LOAD PHASE TABLE */
settable(t3,2,phi3);
settable(t4,1,phx);
if (TROSY[A]=='y')
{settable(t1,1,ph_x);
settable(t9,1,phx);
settable(t10,1,phy);
settable(t11,1,phx);
settable(t12,2,recT);}
else
{settable(t1,1,phx);
settable(t9,8,phi9);
settable(t10,1,phx);
settable(t11,1,phy);
settable(t12,4,rec);}
/* INITIALIZE VARIABLES */
/* maximum fine power for pwC pulses (and initialize rfst) */
rf0 = 4095.0; rfst=0.0;
/* 180 degree adiabatic C13 pulse from 0 to 200 ppm */
if (C13refoc[A]=='y')
{rfst = (compC*4095.0*pwC*4000.0*sqrt((30.0*sfrq/600.0+7.0)/0.35));
rfst = (int) (rfst + 0.5);
if ( 1.0/(4000.0*sqrt((30.0*sfrq/600.0+7.0)/0.35)) < pwC )
{ text_error( " Not enough C13 RF. pwC must be %f usec or less.\n",
(1.0e6/(4000.0*sqrt((30.0*sfrq/600.0+7.0)/0.35))) ); psg_abort(1); }}
/* selective H20 one-lobe sinc pulse */
if(pwHs > 1e-6)
tpwrs = tpwr - 20.0*log10(pwHs/(compH*pw*1.69)); /* needs 1.69 times more */
else /* power than a square pulse */
tpwrs = 0.0;
tpwrs = (int) (tpwrs);
if (tpwrsf<4095.0) tpwrs = tpwrs + 6.0;
if (tpwrsf < 4095.0)
{
tpwrs = tpwrs + 6.0;
pwr_dly = POWER_DELAY + PWRF_DELAY;
}
else pwr_dly = POWER_DELAY;
/* power level for N15 spinlock (90 degree pulse length calculated first) */
slNlvl = 1/(4.0*slNrf*sfrq/600.0) ;
slNlvl = pwNlvl - 20.0*log10(slNlvl/(pwN*compN));
slNlvl = (int) (slNlvl + 0.5);
/* use 1/8J times for relaxation measurements of NH2 groups */
if ( (NH2only[A]=='y') && ((T1[A]=='y') || (T1rho[A]=='y') || (T2[A]=='y')) )
{ tNH = tNH/2.0; }
/* reset calH and calN for 2D if inadvertently left at 2.0 */
if (ni>1.0) {calH=1.0; calN=1.0;}
/* make shapes and set up parameters for HH h**o-decoupling */
if(Cdecflg[0] == 'y') makeCdec();
if(Hdecflg[0] == 'y') makeHHdec();
if(Hdecflg[0] != 'n')
{
pwHH = pwHs;
pwHs = 0.0;
}
/* CHECK VALIDITY OF PARAMETER RANGES */
if ((TROSY[A]=='y') && (gt1 < -2.0e-4 + pwHs + 1.0e-4 + 2.0*POWER_DELAY))
{ text_error( " gt1 is too small. Make gt1 equal to %f or more.\n",
(-2.0e-4 + pwHs + 1.0e-4 + 2.0*POWER_DELAY) ); psg_abort(1); }
if((dm[A] == 'y' || dm[B] == 'y' || dm[C] == 'y' ))
{ text_error("incorrect dec1 decoupler flags! Should be 'nnn' "); psg_abort(1); }
if((dm2[A] == 'y' || dm2[B] == 'y'))
{ text_error("incorrect dec2 decoupler flags! Should be 'nny' "); psg_abort(1); }
if( dpwr2 > 50 )
{ text_error("don't fry the probe, DPWR2 too large! "); psg_abort(1); }
if( pw > 50.0e-6 )
{ text_error("dont fry the probe, pw too high ! "); psg_abort(1); }
if( pwN > 100.0e-6 )
{ text_error("dont fry the probe, pwN too high ! "); psg_abort(1); }
/* RELAXATION TIMES AND FLAGS */
/* evaluate maximum relaxT, relaxTmax chosen by the user */
rTnum = getarray("relaxT", rTarray);
relaxTmax = rTarray[0];
for (rTcounter=1; rTcounter<rTnum; rTcounter++)
if (relaxTmax < rTarray[rTcounter]) relaxTmax = rTarray[rTcounter];
/* compare relaxTmax with maxrelaxT */
if (maxrelaxT > relaxTmax) relaxTmax = maxrelaxT;
if ( ((T1rho[A]=='y') || (T2[A]=='y')) && (relaxTmax > d1) )
{ text_error("Maximum relaxation time, relaxT, is greater than d1 ! "); psg_abort(1);}
if ( ((T1[A]=='y') && (T1rho[A]=='y')) || ((T1[A]=='y') && (T2[A]=='y')) ||
((T1rho[A]=='y') && (T2[A]=='y')) )
{ text_error("Choose only one relaxation measurement ! "); psg_abort(1); }
if ( ((T1[A]=='y') || (T1rho[A]=='y')) &&
((relaxT*100.0 - (int)(relaxT*100.0+1.0e-4)) > 1.0e-6) )
{ text_error("Relaxation time, relaxT, must be zero or multiple of 10msec"); psg_abort(1);}
if ( (T2[A]=='y') &&
(((relaxT+0.01)*50.0 - (int)((relaxT+0.01)*50.0+1.0e-4)) > 1.0e-6) )
{ text_error("Relaxation time, relaxT, must be odd multiple of 10msec"); psg_abort(1);}
if ( ((T1rho[A]=='y') || (T2[A]=='y')) && (relaxTmax > 0.25) && (ix==1) )
{ printf("WARNING, sample heating will result for relaxT>0.25sec"); }
if ( ((T1rho[A]=='y') || (T2[A]=='y')) && (relaxTmax > 0.5) )
{ text_error("relaxT greater than 0.5 seconds will heat sample"); psg_abort(1);}
if ( ((NH2only[A]=='y') || (T1[A]=='y') || (T1rho[A]=='y') || (T2[A]=='y'))
&& (TROSY[A]=='y') )
{ text_error("TROSY not implemented with NH2 spectrum, or relaxation exps."); psg_abort(1);}
if ((TROSY[A]=='y') && (dm2[C] == 'y'))
{ text_error("Choose either TROSY='n' or dm2='n' ! "); psg_abort(1); }
/* PHASES AND INCREMENTED TIMES */
/* Phase incrementation for hypercomplex 2D data, States-Haberkorn element */
if (TROSY[A]=='y')
{ if (phase1 == 2) icosel = -1;
else { tsadd(t4,2,4); tsadd(t10,2,4); icosel = +1; }
}
else { if (phase1 == 2) {tsadd(t10,2,4); icosel = +1;}
else icosel = -1;
}
if(Hdecflg[0] != 'n') ihh = icosel;
/* Set up f1180 */
tau1 = d2;
if((f1180[A] == 'y') && (ni > 1.0))
{ tau1 += ( 1.0 / (2.0*sw1) ); if(tau1 < 0.2e-6) tau1 = 0.0; }
tau1 = tau1/2.0;
/* Calculate modifications to phases for States-TPPI acquisition */
if( ix == 1) d2_init = d2;
t1_counter = (int) ( (d2-d2_init)*sw1 + 0.5 );
if(t1_counter % 2)
{ tsadd(t3,2,4); tsadd(t12,2,4); }
/* Correct inverted signals for NH2 only spectra */
if ((NH2only[A]=='y') && (T1[A]=='n') && (T1rho[A]=='n') && (T2[A]=='n'))
{ tsadd(t3,2,4); }
/* BEGIN PULSE SEQUENCE */
status(A);
obspower(tpwr);
decpower(pwClvl);
decpwrf(rf0);
dec2power(pwNlvl);
txphase(zero);
decphase(zero);
dec2phase(zero);
if(Hdecflg[0] != 'n')
{
delay(5.0e-5);
rgpulse(pw,zero,rof1,0.0);
rgpulse(pw,one,0.0,rof1);
zgradpulse(1.5*gzlvl0, 0.5e-3);
delay(5.0e-4);
rgpulse(pw,zero,rof1,0.0);
rgpulse(pw,one,0.0,rof1);
zgradpulse(-gzlvl0, 0.5e-3);
}
delay(d1);
/* xxxxxxxxxxxxxxxxx CONSTANT SAMPLE HEATING FROM N15 RF xxxxxxxxxxxxxxxxx */
if (T1rho[A]=='y')
{dec2power(slNlvl);
dec2rgpulse(relaxTmax-relaxT, zero, 0.0, 0.0);
dec2power(pwNlvl);}
if (T2[A]=='y')
{ncyc = 8.0*100.0*(relaxTmax - relaxT);
if (BPpwrlimits > 0.5)
{
dec2power(pwNlvl-3.0); /* reduce for probe protection */
pwN=pwN*compN*1.4;
}
if (ncyc > 0)
{initval(ncyc,v1);
loop(v1,v2);
delay(0.625e-3 - pwN);
dec2rgpulse(2*pwN, zero, 0.0, 0.0);
delay(0.625e-3 - pwN);
endloop(v2);}
if (BPpwrlimits > 0.5)
{
dec2power(pwNlvl); /* restore normal value */
pwN=getval("pwN");
}
}
/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
rcvroff();
if (TROSY[A]=='n')
dec2rgpulse(pwN, zero, 0.0, 0.0); /*destroy N15 magnetization*/
zgradpulse(gzlvl0, 0.5e-3);
delay(1.0e-4);
if (TROSY[A]=='n') dec2rgpulse(pwN, one, 0.0, 0.0);
zgradpulse(0.7*gzlvl0, 0.5e-3);
decpwrf(rfst);
txphase(t1);
delay(5.0e-4);
if ( dm3[B] == 'y' ) /* begins optional 2H decoupling */
{
lk_hold();
dec3rgpulse(1/dmf3,one,10.0e-6,2.0e-6);
dec3unblank();
dec3phase(zero);
delay(2.0e-6);
setstatus(DEC3ch, TRUE, 'w', FALSE, dmf3);
}
rgpulse(calH*pw,t1,0.0,0.0); /* 1H pulse excitation */
txphase(zero);
dec2phase(zero);
zgradpulse(gzlvl0, gt0);
delay(lambda - gt0 - pwHH);
if(Hdecflg[0] != 'n')
{
obspower(tpwrs);
if (tpwrsf<4095.0) obspwrf(tpwrsf);
shaped_pulse("H2Osinc", pwHH, two, 5.0e-5, 0.0);
obspower(tpwr);
if (tpwrsf<4095.0) obspwrf(4095.0);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
obspower(tpwrs);
if (tpwrsf<4095.0) obspwrf(tpwrsf);
shaped_pulse("H2Osinc", pwHH, two, 5.0e-5, 0.0);
obspower(tpwr);
if (tpwrsf<4095.0) obspwrf(4095.0);
}
else
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
txphase(one);
zgradpulse(gzlvl0, gt0);
delay(lambda - gt0 - pwHH);
rgpulse(pw, one, 0.0, 0.0);
txphase(two);
obspower(tpwrs);
if (tpwrsf<4095.0) obspwrf(tpwrsf);
shaped_pulse("H2Osinc", pwHs, two, 5.0e-5, 0.0);
obspower(tpwr);
if (tpwrsf<4095.0) obspwrf(4095.0);
if (TROSY[A]=='y')
zgradpulse(ihh*gzlvl3, gt3);
else
zgradpulse(-ihh*gzlvl3, gt3);
dec2phase(t3);
delay(2.0e-4);
dec2rgpulse(calN*pwN, t3, 0.0, 0.0);
txphase(zero);
decphase(zero);
/* xxxxxxxxxxxxxxxxxx OPTIONS FOR N15 RELAXATION xxxxxxxxxxxxxxxxxxxx */
if ( (T1[A]=='y') || (T1rho[A]=='y') || (T2[A]=='y') )
{
dec2phase(one);
zgradpulse(gzlvl4, gt4); /* 2.0*GRADIENT_DELAY */
delay(tNH - gt4 - 2.0*GRADIENT_DELAY);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, one, 0.0, 0.0);
zgradpulse(gzlvl4, gt4); /* 2.0*GRADIENT_DELAY */
delay(tNH - gt4 - 2.0*GRADIENT_DELAY);
}
/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
if (T1[A]=='y')
{
dec2rgpulse(pwN, one, 0.0, 0.0);
dec2phase(three);
zgradpulse(gzlvl0, gt0); /* 2.0*GRADIENT_DELAY */
delay(2.5e-3 - gt0 - 2.0*GRADIENT_DELAY - pw);
rgpulse(2.0*pw, zero, 0.0, 0.0);
delay(2.5e-3 - pw);
ncyc = (100.0*relaxT);
initval(ncyc,v4);
if (ncyc > 0)
{loop(v4,v5);
delay(2.5e-3 - pw);
rgpulse(2.0*pw, two, 0.0, 0.0);
delay(2.5e-3 - pw);
delay(2.5e-3 - pw);
rgpulse(2.0*pw, zero, 0.0, 0.0);
delay(2.5e-3 - pw);
endloop(v5);}
dec2rgpulse(pwN, three, 0.0, 0.0);
}
/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
/* Theory suggests 8.0 is better than 2PI as RF */
/* field multiplier and experiment confirms this.*/
if (T1rho[A]=='y') /* Shift evolution of 2.0*pwN/PI for one pulse */
{ /* at end left unrefocused as for normal sequence*/
delay(1.0/(8.0*slNrf) - pwN);
decrgpulse(pwN, zero, 0.0, 0.0);
dec2power(slNlvl);
/* minimum 5ms spinlock to dephase */
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0); /* spins not locked */
sim3pulse(2.0*pw, 0.0, 2.0*pw, zero, zero, zero, 0.0, 0.0);
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0);
ncyc = 100.0*relaxT;
initval(ncyc,v4); if (ncyc > 0)
{loop(v4,v5);
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0);
sim3pulse(2.0*pw, 0.0, 2.0*pw, two, zero, zero, 0.0, 0.0);
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0);
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0);
sim3pulse(2.0*pw, 0.0, 2.0*pw, zero, zero, zero, 0.0, 0.0);
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0);
endloop(v5);}
dec2power(pwNlvl);
decrgpulse(pwN, zero, 0.0, 0.0);
delay(1.0/(8.0*slNrf) + 2.0*pwN/PI - pwN);
}
/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
if (T2[A]=='y')
{
dec2phase(zero);
initval(0.0,v3); initval(180.0,v4);
if (BPpwrlimits > 0.5)
{
dec2power(pwNlvl-3.0); /* reduce for probe protection */
pwN=pwN*compN*1.4;
}
ncyc = 100.0*relaxT;
initval(ncyc,v5);
loop(v5,v6);
initval(3.0,v7);
loop(v7,v8);
delay(0.625e-3 - pwN);
dec2rgpulse(2.0*pwN, zero, 0.0, 0.0);
delay(0.625e-3 - pwN);
endloop(v8);
delay(0.625e-3 - pwN - SAPS_DELAY);
add(v4,v3,v3); obsstepsize(1.0); xmtrphase(v3); /* SAPS_DELAY */
dec2rgpulse(2.0*pwN, zero, 0.0, 0.0);
delay(0.625e-3 - pwN - pw);
rgpulse(2*pw, zero, 0.0, 0.0);
delay(0.625e-3 - pwN - pw );
dec2rgpulse(2.0*pwN, zero, 0.0, 0.0);
xmtrphase(zero); /* SAPS_DELAY */
delay(0.625e-3 - pwN - SAPS_DELAY);
initval(3.0,v9);
loop(v9,v10);
delay(0.625e-3 - pwN);
dec2rgpulse(2.0*pwN, zero, 0.0, 0.0);
delay(0.625e-3 - pwN);
endloop(v10);
endloop(v6);
if (BPpwrlimits > 0.5)
{
dec2power(pwNlvl); /* restore normal value */
pwN=getval("pwN");
}
}
/* xxxxxxxxxxxxxxxxxx OPTIONS FOR N15 EVOLUTION xxxxxxxxxxxxxxxxxxxxx */
txphase(zero);
dec2phase(t9);
if ( (NH2only[A]=='y') || (T1[A]=='y') || (T1rho[A]=='y') || (T2[A]=='y') )
{
delay(tau1);
/* optional sech/tanh pulse in middle of t1 */
if (C13refoc[A]=='y') /* WFG_START_DELAY */
{decshaped_pulse("stC200", 1.0e-3, zero, 0.0, 0.0);
delay(tNH - 1.0e-3 - WFG_START_DELAY - 2.0*pw);}
else
{delay(tNH - 2.0*pw);}
rgpulse(2.0*pw, zero, 0.0, 0.0);
if (tNH < gt1 + 1.99e-4) delay(gt1 + 1.99e-4 - tNH);
delay(tau1);
dec2rgpulse(2.0*pwN, t9, 0.0, 0.0);
if (mag_flg[A] == 'y') magradpulse(gzcal*gzlvl1, gt1);
else zgradpulse(gzlvl1, gt1); /* 2.0*GRADIENT_DELAY */
txphase(t4);
dec2phase(t10);
if (tNH > gt1 + 1.99e-4) delay(tNH - gt1 - 2.0*GRADIENT_DELAY);
else delay(1.99e-4 - 2.0*GRADIENT_DELAY);
}
else if (TROSY[A]=='y')
{
if ( (C13refoc[A]=='y') && (tau1 > 0.5e-3 + WFG2_START_DELAY) )
{delay(tau1 - 0.5e-3 - WFG2_START_DELAY); /* WFG2_START_DELAY */
decshaped_pulse("stC200", 1.0e-3, zero, 0.0, 0.0);
delay(tau1 - 0.5e-3);}
else delay(2.0*tau1);
if (mag_flg[A] == 'y') magradpulse(gzcal*gzlvl1, gt1);
else zgradpulse(gzlvl1, gt1); /* 2.0*GRADIENT_DELAY */
delay(2.0e-4 - 2.0*GRADIENT_DELAY);
dec2rgpulse(2.0*pwN, t9, 0.0, 0.0);
txphase(three);
delay(gt1 + 2.0e-4 - pwHs - 1.0e-4 - 2.0*pwr_dly);
obspower(tpwrs);
if (tpwrsf<4095.0) obspwrf(tpwrsf);
shaped_pulse("H2Osinc", pwHs, three, 5.0e-5, 0.0);
obspower(tpwr);
if (tpwrsf<4095.0) obspwrf(4095.0);
txphase(t4);
delay(5.0e-5);
}
else
{ /* fully-coupled spectrum */
if (dm2[C]=='n') {rgpulse(2.0*pw, zero, 0.0, 0.0); pw=0.0;}
if ( (C13refoc[A]=='y') && (tau1 > 0.5e-3 + WFG2_START_DELAY) )
{delay(tau1 - 0.5e-3 - WFG2_START_DELAY); /* WFG2_START_DELAY */
simshaped_pulse("", "stC200", 2.0*pw, 1.0e-3, zero, zero, 0.0, 0.0);
delay(tau1 - 0.5e-3);
delay(gt1 + 2.0e-4);}
else
{delay(tau1);
rgpulse(2.0*pw, zero, 0.0, 0.0);
delay(gt1 + 2.0e-4 - 2.0*pw);
delay(tau1);}
pw=getval("pw");
dec2rgpulse(2.0*pwN, t9, 0.0, 0.0);
if (mag_flg[A] == 'y') magradpulse(gzcal*gzlvl1, gt1);
else zgradpulse(gzlvl1, gt1); /* 2.0*GRADIENT_DELAY */
txphase(t4);
dec2phase(t10);
delay(2.0e-4 - 2.0*GRADIENT_DELAY);
}
if (T1rho[A]=='y') delay(POWER_DELAY);
/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
if (TROSY[A]=='y') rgpulse(pw, t4, 0.0, 0.0);
else sim3pulse(pw, 0.0, pwN, t4, zero, t10, 0.0, 0.0);
txphase(zero);
dec2phase(zero);
zgradpulse(gzlvl5, gt5);
if (TROSY[A]=='y') delay(lambda - 0.65*(pw + pwN) - gt5);
else delay(lambda - 1.3*pwN - gt5);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
zgradpulse(gzlvl5, gt5);
txphase(one);
dec2phase(t11);
delay(lambda - 1.3*pwN - gt5);
sim3pulse(pw, 0.0, pwN, one, zero, t11, 0.0, 0.0);
txphase(zero);
dec2phase(zero);
zgradpulse(1.5*gzlvl5, gt5);
delay(lambda - 1.3*pwN - gt5);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
dec2phase(t10);
zgradpulse(1.5*gzlvl5, gt5);
if (TROSY[A]=='y') delay(lambda - 1.6*pwN - gt5);
else delay(lambda - 0.65*pwN - gt5);
if (TROSY[A]=='y') dec2rgpulse(pwN, t10, 0.0, 0.0);
else rgpulse(pw, zero, 0.0, 0.0);
delay((gt1/10.0) + 1.0e-4 +gstab - 0.65*pw + 2.0*GRADIENT_DELAY + POWER_DELAY);
if ( dm3[B] == 'y' ) /* turns off 2H decoupling */
{
setstatus(DEC3ch, FALSE, 'c', FALSE, dmf3);
dec3rgpulse(1/dmf3,three,2.0e-6,2.0e-6);
dec3blank();
lk_autotrig(); /* resumes lock pulsing */
}
rgpulse(2.0*pw, zero, 0.0, 0.0);
dec2power(dpwr2); /* POWER_DELAY */
if (mag_flg[A] == 'y') magradpulse(icosel*gzcal*gzlvl2, 0.1*gt1);
else zgradpulse(icosel*gzlvl2, 0.1*gt1); /* 2.0*GRADIENT_DELAY */
if(Cdecflg[0] == 'y')
{
delay(gstab-2.0*POWER_DELAY-PRG_START_DELAY+rof2);
rcvron();
statusdelay(C,1.0e-4);
if (dm3[B] == 'y')
{
delay(1/dmf3);
lk_sample();
}
setreceiver(t12);
pbox_decon(&Cdseq);
if(Hdecflg[0] == 'y')
homodec(&HHdseq);
}
else
{
delay(gstab+rof2);
rcvron();
statusdelay(C,1.0e-4);
if (dm3[B] == 'y')
{
delay(1/dmf3);
lk_sample();
}
setreceiver(t12);
if(Hdecflg[0] == 'y')
homodec(&HHdseq);
}
}
pulsesequence() {
/* Acquisition variables */
double dw; /* nominal dwell time, = 1/sw */
double aqtm = getval("aqtm");
/* Delay variables */
double tref,
te_delay1, te_delay2, tr_delay, ti_delay,
del1, del2, del3, del4, del5, /* before and after diffusion gradients */
busy1, busy2, /* time spent on rf pulses etc. in TE periods */
seqtime, invTime;
int use_minte;
/* RF and receiver frequency variables */
double freq90[MAXNSLICE],freq180[MAXNSLICE],freqIR[MAXNSLICE]; /* frequencies for multi-slice */
int shape90=0, shape180=0, shapeIR=0; /* List ID for RF shapes */
double roff1, roff2, roffn; /* Receiver offsets when FOV is offset along readout */
/* Gradient amplitudes, may vary depending on "image" parameter */
double peramp, perinc, peamp, roamp, roramp;
/* diffusion variables */
#define MAXDIR 1024 /* Will anybody do more than 1024 directions or b-values? */
int diff_in_one = 0;
double tmp, tmp_ss2;
double roarr[MAXDIR], pearr[MAXDIR], slarr[MAXDIR];
int nbval, /* Total number of bvalues*directions */
nbro, nbpe, nbsl; /* bvalues*directions along RO, PE, and SL */
double bro[MAXDIR], bpe[MAXDIR], bsl[MAXDIR], /* b-values along RO, PE, SL */
brs[MAXDIR], brp[MAXDIR], bsp[MAXDIR], /* the cross-terms */
btrace[MAXDIR], /* and the trace */
max_bval=0,
dcrush, dgss2, /* "delta" for crusher and gss2 gradients */
Dro, Dcrush, Dgss2; /* "DELTA" for readout, crusher and gss2 gradients */
/* loop variable */
int i;
/* Real-time variables used in this sequence **************/
int vms_slices = v3; // Number of slices
int vms_ctr = v4; // Slice loop counter
int vnseg = v5; // Number of segments
int vnseg_ctr = v6; // Segment loop counter
int vetl = v7; // Number of choes in readout train
int vetl_ctr = v8; // etl loop counter
int vblip = v9; // Sign on blips in multi-shot experiment
int vssepi = v10; // Number of Gradient Steady States lobes
int vssepi_ctr = v11; // Steady State counter
int vacquire = v12; // Argument for setacqvar, to skip steady states
/******************************************************/
/* VARIABLE INITIALIZATIONS ***************************/
/******************************************************/
get_parameters();
euler_test();
if (tep < 0) { // adjust by reducing gpropdelay by that amount
gpropdelay += tep;
tep = 0;
}
setacqmode(WACQ|NZ); // Necessary for variable rate sampling
use_minte = (minte[0] == 'y');
/******************************************************/
/* CALCULATIONS ***************************************/
/******************************************************/
if (ix == 1) {
/* Calculate RF pulse */
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
calc_rf(&p1_rf,"tpwr1","tpwr1f");
/* Calculate gradients: */
init_slice(&ss_grad,"ss",thk);
calc_slice(&ss_grad, &p1_rf,WRITE,"gss");
init_slice_refocus(&ssr_grad,"ssr");
calc_slice_refocus(&ssr_grad, &ss_grad, WRITE,"gssr");
if (spinecho[0] == 'y') {
init_rf(&p2_rf,p2pat,p2,flip2,rof1,rof1);
calc_rf(&p2_rf,"tpwr2","tpwr2f");
init_slice_butterfly(&ss2_grad,"ss2",thk,gcrush,tcrush);
calc_slice(&ss2_grad,&p2_rf,WRITE,"gss2");
}
else ss2_grad.duration = 0; /* used for diffusion calculations */
init_readout(&epiro_grad,"epiro",lro,np,sw);
init_readout_refocus(&ror_grad,"ror");
init_phase(&epipe_grad, "epipe",lpe,nv);
init_phase(&per_grad,"per",lpe,nv);
init_readout(&nav_grad,"nav",lro,np,sw);
init_epi(&epi_grad);
if (!strcmp(orient,"oblique")) {
if ((phi != 90) || (psi != 90) || (theta != 90)) {
/* oblique slice - this should take care of most cases */
epiro_grad.slewRate /= 3; /* = gmax/trise */
epipe_grad.slewRate /= 3;
}
}
calc_epi(&epi_grad,&epiro_grad,&epipe_grad,&ror_grad,&per_grad,&nav_grad,NOWRITE);
/* Make sure the slice refocus, readout refocus,
and phase dephaser fit in the same duration */
tref = calc_sim_gradient(&ror_grad, &per_grad, &null_grad, getval("tpe"), WRITE);
if (sgldisplay) displayEPI(&epi_grad);
/* calc_sim_gradient recalculates per_grad, so reset its
base amplitude for centric ordering or fractional k-space*/
switch(ky_order[0]) {
case 'l':
per_grad.amp *= (fract_ky/(epipe_grad.steps/2));
break;
case 'c':
per_grad.amp = (nseg/2-1)*per_grad.increment;
break;
}
if (ir[0] == 'y') {
init_rf(&ir_rf,pipat,pi,flipir,rof1,rof1);
calc_rf(&ir_rf,"tpwri","tpwrif");
init_slice_butterfly(&ssi_grad,"ssi",thk,gcrush,tcrush);
calc_slice(&ssi_grad,&ir_rf,WRITE,"gssi");
}
if (fsat[0] == 'y') {
create_fatsat();
}
if (diff[0] == 'y') {
init_generic(&diff_grad,"diff",gdiff,tdelta);
diff_grad.maxGrad = gmax;
calc_generic(&diff_grad,NOWRITE,"","");
/* adjust duration, so tdelta is from start ramp up to start ramp down */
if (ix == 1) {
diff_grad.duration += diff_grad.tramp;
calc_generic(&diff_grad,WRITE,"","");
}
}
/* Acquire top-down or bottom-up ? */
if (ky_order[1] == 'r') {
epipe_grad.amp *= -1;
per_grad.amp *= -1;
per_grad.increment *= -1;
}
} /* end gradient setup if ix == 1 */
/* Load table used to determine multi-shot direction */
settable(t2,(int) nseg,epi_grad.table2);
/* What is happening in the 2 TE/2 periods (except for diffusion)? */
busy1 = ss_grad.rfCenterBack + ssr_grad.duration;
busy2 = tep + nav_grad.duration*(epi_grad.center_echo + 0.5);
if (navigator[0] == 'y')
busy2 += (tep + nav_grad.duration + per_grad.duration);
/* How much extra time do we have in each TE/2 period? */
if (spinecho[0] == 'y') {
busy1 += (GDELAY + ss2_grad.rfCenterFront);
busy2 += ss2_grad.rfCenterBack;
temin = MAX(busy1,busy2)*2;
if (use_minte) te = temin;
te_delay1 = te/2 - busy1;
te_delay2 = te/2 - busy2;
if (temin > te) { /* Use min TE and try and catch further violations of min TE */
te_delay1 = temin/2 - busy1;
te_delay2 = temin/2 - busy2;
}
}
else { /* Gradient echo */
temin = (busy1 + busy2);
if (use_minte) te = temin;
te_delay1 = te - temin;
te_delay2 = 0;
if (temin > te) te_delay1 = 0;
}
/* Now fill in the diffusion delays:
del1 = between 90 and 1st diffusion gradient
del2 = after 1st diffusion gradient
del3 = before 2nd diffusion gradient when both in same TE/2 period
del4 = before 2nd diffusion gradient when in different TE/2 period
del5 = before acquisition
Ie, the order is:
90 - del1 - diff - del2 - (diff - del3) - 180 - (del4 - diff) - del5 - acq
where one and only one of the two options (diff - del3) or (del4 - diff) is used
*/
if (diff[0] == 'y') {
tmp_ss2 = GDELAY + ss2_grad.duration; /* ss2 grad + 4us delay */
del1 = del2 = del3 = del4 = del5 = 0;
if (tDELTA < (diff_grad.duration + tmp_ss2)) /* Minimum DELTA */
abort_message("ERROR %s: tDELTA is too short, minimum is %.2fms\n",
seqfil,(diff_grad.duration + tmp_ss2)*1000+0.005);
if (tDELTA + diff_grad.duration > te_delay1 + tmp_ss2 + te_delay2) {
if (!use_minte) {
abort_message("ERROR %s: Maximum tDELTA is %.2fms",
seqfil,te_delay1 + ss2_grad.duration + te_delay2 - diff_grad.duration);
}
else {
tmp = (tDELTA + diff_grad.duration) - (te_delay1 + tmp_ss2 + te_delay2);
if (spinecho[0] == 'y') {
te_delay1 += (tmp/2);
te_delay2 += (tmp/2);
}
else
te_delay1 += tmp;
temin += tmp;
}
}
if (spinecho[0] == 'y') {
if (te_delay1 >= (tDELTA + diff_grad.duration)) { /* Put them both in 1st TE/2 period, */
diff_in_one = (diff[0] == 'y'); /* no need to increase temin */
del2 = tDELTA - diff_grad.duration; /* time between diffusion gradients */
del3 = te_delay1 - (tDELTA+diff_grad.duration); /* time after diffusion gradients */
del5 = te_delay2; /* delay in second TE/2 period */
}
else { /* put them on each side of the 180 */
diff_in_one = 0;
busy1 += diff_grad.duration;
busy2 += diff_grad.duration;
temin = 2*MAX(busy1,busy2);
/* Optimally, the 2nd diff grad is right after the 180 */
del2 = tDELTA - diff_grad.duration - tmp_ss2; /* This is always > 0, or we would have aborted above */
del1 = te_delay1 - (diff_grad.duration + del2);
if (del1 < 0) {
del1 = 0; /* Place the 1st right after the 90 and push the 2nd out */
del4 = tDELTA - te_delay1 - ss2_grad.duration;
}
del5 = te_delay2 - (del4 + diff_grad.duration);
/* del5 could still be < 0, when te_delay2 < diff_grad.duration */
if (del5 < 0) {
del1 += fabs(del5); /* Increase each TE/2 period by abs(del5) */
del5 = 0;
}
}
}
else { /* gradient echo */
diff_in_one = (diff[0] == 'y');
del1 = 0;
del2 = tDELTA - diff_grad.duration; /* time between diffusion gradients */
del3 = 0;
del4 = 0;
if (!use_minte) /* user defined TE */
del5 = te_delay1 - (tDELTA + diff_grad.duration);
}
} /* End of Diffusion block */
else {
del1 = te_delay1;
del5 = te_delay2;
del2 = del3 = del4 = 0;
}
if (sgldisplay) {
text_message("busy1/2, temin = %f, %f, %f",busy1*1e3, busy2*1e3, temin*1e3);
text_message("te_delay1/2 = %f, %f",te_delay1*1e3, te_delay2*1e3);
text_message("delays 1-5: %.2f, %.2f, %.2f, %.2f, %.2fms\n",del1*1000,del2*1000,del3*1000,del4*1000,del5*1000);
}
/* Check if TE is long enough */
temin = ceil(temin*1e6)/1e6; /* round to nearest us */
if (use_minte) {
te = temin;
putvalue("te",te);
}
else if (temin > te) {
abort_message("TE too short, minimum is %.2f ms\n",temin*1000);
}
if (ir[0] == 'y') {
ti_delay = ti - (pi*ssi_grad.rfFraction + rof2 + ssi_grad.rfDelayBack)
- (ss_grad.rfDelayFront + rof1 + p1*(1-ss_grad.rfFraction));
if (ti_delay < 0) {
abort_message("TI too short, minimum is %.2f ms\n",(ti-ti_delay)*1000);
}
}
else ti_delay = 0;
invTime = GDELAY + ssi_grad.duration + ti_delay;
/* Minimum TR per slice, w/o options */
seqtime = GDELAY + ss_grad.rfCenterFront // Before TE
+ te
+ (epiro_grad.duration - nav_grad.duration*(epi_grad.center_echo+0.5)); // After TE
/* Add in time for options outside of TE */
if (ir[0] == 'y') seqtime += invTime;
if (fsat[0] == 'y') seqtime += fsatTime;
trmin = seqtime + 4e-6; /* ensure a minimum of 4us in tr_delay */
trmin *= ns;
if (tr - trmin < 0.0) {
abort_message("%s: Requested tr too short. Min tr = %.2f ms\n",
seqfil,ceil(trmin*100000)/100.00);
}
/* spread out multi-slice acquisition over total TR */
tr_delay = (tr - ns*seqtime)/ns;
/******************************************************/
/* Return gradient values to VnmrJ interface */
/******************************************************/
putvalue("etl",epi_grad.etl+2*ssepi);
putvalue("gro",epiro_grad.amp);
putvalue("rgro",epiro_grad.tramp);
putvalue("gror",ror_grad.amp);
putvalue("tror",ror_grad.duration);
putvalue("rgror",ror_grad.tramp);
putvalue("gpe",epipe_grad.amp);
putvalue("rgpe",epipe_grad.tramp);
putvalue("gped",per_grad.amp);
putvalue("tped",per_grad.duration);
putvalue("rgped",per_grad.tramp);
putvalue("gss",ss_grad.amp);
putvalue("gss2",ss2_grad.ssamp);
putvalue("rgss",ss_grad.tramp);
putvalue("gssr",ssr_grad.amp);
putvalue("tssr",ssr_grad.duration);
putvalue("rgssr",ssr_grad.tramp);
putvalue("rgss2",ss2_grad.crusher1RampToSsDuration);
putvalue("rgssi",ssi_grad.crusher1RampToSsDuration);
putvalue("rgcrush",ssi_grad.crusher1RampToCrusherDuration);
putvalue("at_full",epi_grad.duration);
putvalue("at_one",nav_grad.duration);
putvalue("rcrush",ss2_grad.crusher1RampToCrusherDuration);
putvalue("np_ramp",epi_grad.np_ramp);
putvalue("np_flat",epi_grad.np_flat);
if (diff[0] == 'y') { /* CALCULATE B VALUES */
/* Get multiplication factors and make sure they have same # elements */
/* All this is only necessary because putCmd only work for ix==1 */
nbro = (int) getarray("dro",roarr); nbval = nbro;
nbpe = (int) getarray("dpe",pearr); if (nbpe > nbval) nbval = nbpe;
nbsl = (int) getarray("dsl",slarr); if (nbsl > nbval) nbval = nbsl;
if ((nbro != nbval) && (nbro != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (readout)",seqfil);
if ((nbpe != nbval) && (nbpe != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (phase)",seqfil);
if ((nbsl != nbval) && (nbsl != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (slice)",seqfil);
if (nbro == 1) for (i = 1; i < nbval; i++) roarr[i] = roarr[0];
if (nbpe == 1) for (i = 1; i < nbval; i++) pearr[i] = pearr[0];
if (nbsl == 1) for (i = 1; i < nbval; i++) slarr[i] = slarr[0];
}
else {
nbval = 1;
roarr[0] = 0;
pearr[0] = 0;
slarr[0] = 0;
}
for (i = 0; i < nbval; i++) {
/* We need to worry about slice gradients & crushers for slice gradients */
/* Everything else is outside diffusion gradients, and thus constant */
/* for all b-values/directions */
/* Readout */
bro[i] = bval(gdiff*roarr[i],tdelta,tDELTA);
/* Phase */
bpe[i] = bval(gdiff*pearr[i],tdelta,tDELTA);
/* Slice */
dgss2 = p2/2; Dgss2 = dgss2;
dcrush = tcrush; Dcrush = dcrush + p2;
bsl[i] = bval(gdiff*slarr[i],tdelta,tDELTA);
if (spinecho[0] == 'y') {
bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval(gcrush,dcrush,Dcrush);
bsl[i] += bval_nested(gcrush,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2);
}
if (!diff_in_one) {
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
}
/* Readout/Slice Cross-terms */
brs[i] = bval2(gdiff*roarr[i],gdiff*slarr[i],tdelta,tDELTA);
if (spinecho[0] == 'y') {
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
}
/* Readout/Phase Cross-terms */
brp[i] = bval2(gdiff*roarr[i],gdiff*pearr[i],tdelta,tDELTA);
/* Slice/Phase Cross-terms */
bsp[i] = bval2(gdiff*slarr[i],gdiff*pearr[i],tdelta,tDELTA);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
btrace[i] = (bro[i]+bsl[i]+bpe[i]);
if (max_bval < btrace[i]) {
max_bval = (bro[i]+bsl[i]+bpe[i]);
}
} /* End for-all-directions */
putarray("bvalrr",bro,nbval);
putarray("bvalpp",bpe,nbval);
putarray("bvalss",bsl,nbval);
putarray("bvalrp",brp,nbval);
putarray("bvalrs",brs,nbval);
putarray("bvalsp",bsp,nbval);
putarray("bvalue",btrace,nbval);
putvalue("max_bval",max_bval);
/* Set all gradients depending on whether we do */
/* Use separate variables, because we only initialize & calculate gradients for ix==1 */
peamp = epipe_grad.amp;
perinc = per_grad.increment;
peramp = per_grad.amp;
roamp = epiro_grad.amp;
roramp = ror_grad.amp;
switch ((int)image) {
case 1: /* Real image scan, don't change anything */
break;
case 0: /* Normal reference scan */
peamp = 0;
perinc = 0;
peramp = 0;
roamp = epiro_grad.amp;
roramp = ror_grad.amp;
break;
case -1: /* Inverted image scan */
roamp = -epiro_grad.amp;
roramp = -ror_grad.amp;
break;
case -2: /* Inverted reference scan */
peamp = 0;
perinc = 0;
peramp = 0;
roamp = -epiro_grad.amp;
roramp = -ror_grad.amp;
break;
default: break;
}
/* Generate phase-ramped pulses: 90, 180, and IR */
offsetlist(pss,ss_grad.ssamp,0,freq90,ns,seqcon[1]);
shape90 = shapelist(p1pat,ss_grad.rfDuration,freq90,ns,0,seqcon[1]);
if (spinecho[0] == 'y') {
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shape180 = shapelist(p2pat,ss2_grad.rfDuration,freq180,ns,0,seqcon[1]);
}
if (ir[0] == 'y') {
offsetlist(pss,ssi_grad.ssamp,0,freqIR,ns,seqcon[1]);
shapeIR = shapelist(pipat,ssi_grad.rfDuration,freqIR,ns,0,seqcon[1]);
}
sgl_error_check(sglerror);
roff1 = -poffset(pro,epi_grad.amppos);
roff2 = -poffset(pro,epi_grad.ampneg);
roffn = -poffset(pro,nav_grad.amp);
roff1 = -poffset(pro,epi_grad.amppos*roamp/epiro_grad.amp);
roff2 = -poffset(pro,epi_grad.ampneg*roamp/epiro_grad.amp);
roffn = -poffset(pro,nav_grad.amp);
dw = granularity(1/sw,1/epi_grad.ddrsr);
/* Total Scan Time */
g_setExpTime(tr*nt*nseg*arraydim);
/******************************************************/
/* PULSE SEQUENCE *************************************/
/******************************************************/
rotate();
F_initval(epi_grad.etl/2, vetl);
/* vetl is the loop counter in the acquisition loop */
/* that includes both a positive and negative readout lobe */
F_initval(nseg, vnseg);
/* NB. F_initval(-ssepi,vssepi); currently gives errors */
initval(-ssepi,vssepi); /* gradient steady state lobes */
obsoffset(resto); delay(GDELAY);
ifzero(rtonce); grad_advance(gpropdelay); endif(rtonce);
loop(vnseg,vnseg_ctr); /* Loop through segments in segmented EPI */
msloop(seqcon[1],ns,vms_slices,vms_ctr); /* Multislice loop */
assign(vssepi,vssepi_ctr);
sp1on(); delay(4e-6); sp1off(); /* Output trigger to look at scope */
if (ticks) {
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
}
getelem(t2,vnseg_ctr,vblip); /* vblip = t2[vnseg_ctr]; either 1 or -1 for pos/neg blip */
/* Optional FAT SAT */
if (fsat[0] == 'y') {
fatsat();
}
/* Optional IR + TI delay */
if (ir[0] == 'y') {
obspower(ir_rf.powerCoarse);
obspwrf(ir_rf.powerFine);
delay(GDELAY);
obl_shapedgradient(ssi_grad.name,ssi_grad.duration,0.0,0.0,ssi_grad.amp,NOWAIT);
delay(ssi_grad.rfDelayBack);
shapedpulselist(shapeIR,ssi_grad.rfDuration,oph,rof1,rof1,seqcon[1],vms_ctr);
delay(ssi_grad.rfDelayBack);
delay(ti_delay);
}
/* 90 ss degree pulse */
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(GDELAY);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0.0,0.0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shape90,p1_rf.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Slice refocus */
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0,0,-ssr_grad.amp,WAIT);
delay(del1);
if (diff[0] == 'y')
obl_shapedgradient(diff_grad.name,diff_grad.duration,
diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
delay(del2);
if (diff_in_one)
obl_shapedgradient(diff_grad.name,diff_grad.duration,
-diff_grad.amp*dro,-diff_grad.amp*dpe,-diff_grad.amp*dsl,WAIT);
delay(del3);
/* Optional 180 ss degree pulse with crushers */
if (spinecho[0] == 'y') {
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(GDELAY);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0.0,0.0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shape180,ss2_grad.rfDuration,oph,rof1,rof1,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
}
delay(del4);
if ((diff[0] == 'y') && !diff_in_one)
obl_shapedgradient(diff_grad.name,diff_grad.duration,
diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
delay(del5);
/* Optional navigator echo */
if (navigator[0] == 'y') {
obl_shapedgradient(ror_grad.name,ror_grad.duration,roramp,0,0,WAIT);
obl_shapedgradient(nav_grad.name,nav_grad.duration,
-nav_grad.amp,0,0,NOWAIT);
delay(tep);
roff = roffn; /* Set receiver offset for navigator gradient */
delay(epi_grad.skip-alfa); /* ramp up */
startacq(alfa);
for(i=0;i<np/2;i++){
sample(dw);
delay((epi_grad.dwell[i] - dw));
}
sample(aqtm-at);
endacq();
delay(epi_grad.skip - dw - (aqtm-at));
/* Phase encode dephaser here if navigator echo was acquired */
var_shapedgradient(per_grad.name,per_grad.duration,0,-peramp,0,perinc,vnseg_ctr,WAIT);
}
else {
var_shapedgradient(per_grad.name,per_grad.duration,
-roramp,-peramp,0,perinc,vnseg_ctr,WAIT);
}
/* Start readout and phase encode gradient waveforms, NOWAIT */
/* If alternating ky-ordering, get polarity on blips from table */
var_shaped3gradient(epiro_grad.name,epipe_grad.name,"", /* patterns */
epiro_grad.duration, /* duration */
roamp,0,0, /* amplitudes */
peamp,vblip, /* step and multiplier */
NOWAIT); /* Don't wait */
delay(tep);
/* Acquisition loop */
assign(one,vacquire); // real-time acquire flag
nowait_loop(epi_grad.etl/2 + ssepi,vetl,vetl_ctr);
ifzero(vssepi_ctr); //vssepi_ctr = -ssepi, -ssepi+1, ..., 0, 1,2,...
assign(zero,vacquire); // turn on acquisition after all ss lobes
endif(vssepi_ctr);
incr(vssepi_ctr);
setacqvar(vacquire); // Set acquire flag
roff = roff1; /* Set receiver offset for positive gradient */
delay(epi_grad.skip-alfa); /* ramp up */
startacq(alfa);
for(i=0;i<np/2;i++){
sample(dw); //dw = 1/sw
delay((epi_grad.dwell[i] - dw));
}
if (aqtm > at) sample(aqtm-at);
endacq();
delay(epi_grad.skip - dw - (aqtm-at));
roff = roff2; /* Set receiver offset for negative gradient */
delay(epi_grad.skip-alfa);
startacq(alfa);
for(i=0;i<np/2;i++){
sample(dw);
delay((epi_grad.dwell[i] - dw));
}
if (aqtm > at) sample(aqtm-at);
endacq();
delay(epi_grad.skip - dw - (aqtm-at));
nowait_endloop(vetl_ctr);
delay(tr_delay);
endmsloop(seqcon[1],vms_ctr); /* end multislice loop */
endloop(vnseg_ctr); /* end segments loop */
} /* end pulsesequence */
/**************************************************************
initparms_img()
Read in all parameters used by the Imaging
SEQD applications package. Build the array
of slice positions used in multislice loops.
*************************************************************/
void initparms_img()
{
int k; /*index for loops*/
/*-------------------------------------------------------------
INITIALIZE PARAMETERS
-------------------------------------------------------------*/
/*--------------------------------------
RFPULSES
--------------------------------------*/
p2 = getvalnwarn("p2");
p3 = getvalnwarn("p3");
p4 = getvalnwarn("p4");
p5 = getvalnwarn("p5");
pi = getvalnwarn("pi");
psat = getvalnwarn("psat");
pmt = getvalnwarn("pmt");
pwx2 = getvalnwarn("pwx2");
psl = getvalnwarn("psl");
getstrnwarn("pwpat",pwpat);
getstrnwarn("p1pat",p1pat);
getstrnwarn("p2pat",p2pat);
getstrnwarn("p3pat",p3pat);
getstrnwarn("p4pat",p4pat);
getstrnwarn("p5pat",p5pat);
getstrnwarn("pipat",pipat);
getstrnwarn("satpat",satpat);
getstrnwarn("mtpat",mtpat);
getstrnwarn("pslpat",pslpat);
tpwr1 = getvalnwarn("tpwr1");
tpwr2 = getvalnwarn("tpwr2");
tpwr3 = getvalnwarn("tpwr3");
tpwr4 = getvalnwarn("tpwr4");
tpwr5 = getvalnwarn("tpwr5");
tpwri = getvalnwarn("tpwri");
mtpwr = getvalnwarn("mtpwr");
pwxlvl2 = getvalnwarn("pwxlvl2");
tpwrsl = getvalnwarn("tpwrsl");
/*--------------------------------------
DECOUPLER PULSES
--------------------------------------*/
getstrnwarn("decpat",decpat);
getstrnwarn("decpat1",decpat1);
getstrnwarn("decpat2",decpat2);
getstrnwarn("decpat3",decpat3);
getstrnwarn("decpat4",decpat4);
getstrnwarn("decpat5",decpat5);
dpwr = getvalnwarn("dpwr");
dpwr1 = getvalnwarn("dpwr1");
dpwr4 = getvalnwarn("dpwr4");
dpwr5 = getvalnwarn("dpwr5");
/*--------------------------------------
GRADIENTS
--------------------------------------*/
gradunit = getvalnwarn("gradunit");
gro = getvalnwarn("gro");
gro2 = getvalnwarn("gro2");
gro3 = getvalnwarn("gro3");
gpe = getvalnwarn("gpe");
gpe2 = getvalnwarn("gpe2");
gpe3 = getvalnwarn("gpe3");
gss = getvalnwarn("gss");
gss2 = getvalnwarn("gss2");
gss3 = getvalnwarn("gss3");
gror = getvalnwarn("gror");
gssr = getvalnwarn("gssr");
grof = getvalnwarn("grof");
gssf = getvalnwarn("gssf");
g0 = getvalnwarn("g0");
g1 = getvalnwarn("g1");
g2 = getvalnwarn("g2");
g3 = getvalnwarn("g3");
g4 = getvalnwarn("g4");
g5 = getvalnwarn("g5");
g6 = getvalnwarn("g6");
g7 = getvalnwarn("g7");
g8 = getvalnwarn("g8");
g9 = getvalnwarn("g9");
gx = getvalnwarn("gx");
gy = getvalnwarn("gy");
gz = getvalnwarn("gz");
gvox1 = getvalnwarn("gvox1");
gvox2 = getvalnwarn("gvox2");
gvox3 = getvalnwarn("gvox3");
gdiff = getvalnwarn("gdiff");
gflow = getvalnwarn("gflow");
gspoil = getvalnwarn("gspoil");
gspoil2 = getvalnwarn("gspoil2");
gcrush = getvalnwarn("gcrush");
gcrush2 = getvalnwarn("gcrush2");
gtrim = getvalnwarn("gtrim");
gtrim2 = getvalnwarn("gtrim2");
gramp = getvalnwarn("gramp");
gramp2 = getvalnwarn("gramp2");
gxscale = getvalnwarn("gxscale");
gyscale = getvalnwarn("gyscale");
gzscale = getvalnwarn("gzscale");
gpemult = getvalnwarn("gpemult");
/* Get gmax or gxmax, gymax, gzmax */
if ( P_getreal(CURRENT,"gxmax",&gxmax,1) < 0 )
{
if ( P_getreal(CURRENT,"gmax",&gmax,1) < 0 )
{
gmax = 0;
}
gxmax = gmax;
}
if ( P_getreal(CURRENT,"gymax",&gymax,1) < 0 )
{
if ( P_getreal(CURRENT,"gmax",&gmax,1) < 0 )
{
gmax = 0;
}
gymax = gmax;
}
if ( P_getreal(CURRENT,"gzmax",&gzmax,1) < 0 )
{
if ( P_getreal(CURRENT,"gmax",&gmax,1) < 0 )
{
gmax = 0;
}
gzmax = gmax;
}
if (gxmax < gzmax)
if (gxmax < gymax)
gmax = gxmax;
else
gmax = gymax;
else
if (gxmax < gymax)
gmax = gxmax;
else
gmax = gymax;
/* --- Get gradient limit parameters --- */
if ( P_getreal(CURRENT,"gtotlimit",>otlimit,1) < 0 )
gtotlimit = gxmax + gymax + gzmax;
if (gtotlimit <= 0.0) gtotlimit = gxmax + gymax + gzmax;
if ( P_getreal(CURRENT,"gxlimit",&gxlimit,1) < 0 )
gxlimit = gxmax;
if (gxlimit <= 0.0) gxlimit = gxmax;
if ( P_getreal(CURRENT,"gylimit",&gylimit,1) < 0 )
gylimit = gymax;
if (gylimit <= 0.0) gylimit = gymax;
if ( P_getreal(CURRENT,"gzlimit",&gzlimit,1) < 0 )
gzlimit = gzmax;
if (gzlimit <= 0.0) gzlimit = gzmax;
/* --- Get gradstepsz if Present --- */
/* if gradstepsz is 32767 gradient waveshaping is being used */
if ( P_getreal(GLOBAL,"gradstepsz",&gradstepsz,1) >= 0 )
{
if (gradstepsz < 1.0)
{
if ((anygradcrwg) || (anygradwg) || (anypfga) || (anypfgw))
gradstepsz = 32767.0;
else
gradstepsz = 2047.0;
}
}
else
{
if ((anygradcrwg) || (anygradwg) || (anypfga) || (anypfgw))
gradstepsz = 32767.0;
else
gradstepsz = 2047.0;
}
getstrnwarn("gpatup",gpatup);
getstrnwarn("gpatdown",gpatdown);
getstrnwarn("gropat",gropat);
getstrnwarn("gpepat",gpepat);
getstrnwarn("gsspat",gsspat);
getstrnwarn("gpat",gpat);
getstrnwarn("gpat1",gpat1);
getstrnwarn("gpat2",gpat2);
getstrnwarn("gpat3",gpat3);
getstrnwarn("gpat4",gpat4);
getstrnwarn("gpat5",gpat5);
/*--------------------------------------
DELAYS
--------------------------------------*/
tr = getvalnwarn("tr");
te = getvalnwarn("te");
ti = getvalnwarn("ti");
tm = getvalnwarn("tm");
at = getvalnwarn("at");
tpe = getvalnwarn("tpe");
tpe2 = getvalnwarn("tpe2");
tpe3 = getvalnwarn("tpe3");
tcrush = getvalnwarn("tcrush");
tdiff = getvalnwarn("tdiff");
tdelta = getvalnwarn("tdelta");
tDELTA = getvalnwarn("tDELTA");
tflow = getvalnwarn("tflow");
tspoil = getvalnwarn("tspoil");
hold = getvalnwarn("hold");
trise = getvalnwarn("trise");
if (trise > 10e-3) abort_message("trise: %5.0f usec is excessive!",trise*1e6);
/*--------------------------------------
FREQUENCIES
--------------------------------------*/
resto = getvalnwarn("resto");
wsfrq = getvalnwarn("wsfrq");
chessfrq = getvalnwarn("chessfrq");
mtfrq = getvalnwarn("mtfrq");
/*--------------------------------------
PHYSICAL POSITIONS AND FOV
--------------------------------------*/
fovunit = getvalnwarn("fovunit");
pro = getvalnwarn("pro");
ppe = getvalnwarn("ppe");
ppe2 = getvalnwarn("ppe2");
ppe3 = getvalnwarn("ppe3");
pos1 = getvalnwarn("pos1");
pos2 = getvalnwarn("pos2");
pos3 = getvalnwarn("pos3");
lro = getvalnwarn("lro");
lpe = getvalnwarn("lpe");
lpe2 = getvalnwarn("lpe2");
lpe3 = getvalnwarn("lpe3");
lss = getvalnwarn("lss");
/*--------------------------------------
PHYSICAL SIZES
--------------------------------------*/
thkunit = getvalnwarn("thkunit");
vox1 = getvalnwarn("vox1");
vox2 = getvalnwarn("vox2");
vox3 = getvalnwarn("vox3");
thk = getvalnwarn("thk");
/*--------------------------------------
BANDWIDTHS
--------------------------------------*/
sw1 = getvalnwarn("sw1");
sw2 = getvalnwarn("sw2");
sw3 = getvalnwarn("sw3");
/*--------------------------------------
ORIENTATION PARAMETERS
--------------------------------------*/
getstrnwarn("orient",orient);
getstrnwarn("vorient",vorient);
getstrnwarn("dorient",dorient);
getstrnwarn("sorient",sorient);
getstrnwarn("orient2",orient2);
psi = getvalnwarn("psi");
phi = getvalnwarn("phi");
theta = getvalnwarn("theta");
vpsi = getvalnwarn("vpsi");
vphi = getvalnwarn("vphi");
vtheta = getvalnwarn("vtheta");
dpsi = getvalnwarn("dpsi");
dphi = getvalnwarn("dphi");
dtheta = getvalnwarn("dtheta");
spsi = getvalnwarn("spsi");
sphi = getvalnwarn("sphi");
stheta = getvalnwarn("stheta");
offsetx = getvalnwarn("offsetx");
offsety = getvalnwarn("offsety");
offsetz = getvalnwarn("offsetz");
gxdelay = getvalnwarn("gxdelay");
gydelay = getvalnwarn("gydelay");
gzdelay = getvalnwarn("gzdelay");
/*--------------------------------------
COUNTS AND FLAGS
--------------------------------------*/
nD = getvalnwarn("nD");
ns = getvalnwarn("ns");
ne = getvalnwarn("ne");
ni = getvalnwarn("ni");
nv = getvalnwarn("nv");
nv2 = getvalnwarn("nv2");
nv3 = getvalnwarn("nv3");
ssc = getvalnwarn("ssc");
ticks = getvalnwarn("ticks");
getstrnwarn("ir",ir);
getstrnwarn("ws",ws);
getstrnwarn("mt",mt);
getstrnwarn("pilot",pilot);
getstrnwarn("seqcon",seqcon);
getstrnwarn("petable",petable);
getstrnwarn("acqtype",acqtype);
getstrnwarn("exptype",exptype);
getstrnwarn("apptype",apptype);
getstrnwarn("seqfil",seqfil);
getstrnwarn("rfspoil",rfspoil);
getstrnwarn("verbose",verbose);
/*--------------------------------------
Miscellaneous
--------------------------------------*/
rfphase = getvalnwarn("rfphase");
B0 = getvalnwarn("B0");
gpropdelay = getvalnwarn("gpropdelay");
kzero = getvalnwarn("kzero");
aqtm = getvalnwarn("aqtm");
getstrnwarn("volumercv",volumercv);
/*--------------------------------------
Build slice position array
--------------------------------------*/
if (ns > MAXSLICE) {
text_error("ns exceeds maximum limit.\n");
psg_abort(1);
}
for (k = 0; k < MAXSLICE; k++) {
pss[k] = 0.0;
}
if (seqcon[1] == 's')
pss[0] = getval("pss");
else if (seqcon[1] == 'c')
getarray("pss",pss);
else
pss[0] = getvalnwarn("pss"); /* get it anyway but with no warning */
/*--------------------------------------
Old SISCO Imaging Parameters
--------------------------------------*/
slcto = getvalnwarn("slcto"); /* slice selection offset */
delto = getvalnwarn("delto"); /* slice spacing frequency */
tox = getvalnwarn("tox");
toy = getvalnwarn("toy");
toz = getvalnwarn("toz");
griserate = getvalnwarn("griserate");
}
void pulsesequence() {
/* Internal variable declarations *************************/
int shapelist90,shapelist180;
double seqtime,tau1,tau2,tau3,te1_delay,te2_delay,te3_delay,tr_delay;
double freq90[MAXNSLICE], freq180[MAXNSLICE];
/* Diffusion variables */
double te1, te1min, del1, del2, del3, del4;
double te_diff1, te_diff2, tmp1, tmp2;
double diffamp;
char diffpat[MAXSTR];
/* Navigator variables */
double etlnav;
/* Variable crushers */
double cscale;
double vcrush; // flag
/* Diffusion parameters */
#define MAXDIR 1024 /* Will anybody do more than 1024 directions or b-values? */
double roarr[MAXDIR], pearr[MAXDIR], slarr[MAXDIR];
int nbval, /* Total number of bvalues*directions */
nbro, nbpe, nbsl,
i;
double bro[MAXDIR], bpe[MAXDIR], bsl[MAXDIR], /* b-values along RO, PE, SL */
brs[MAXDIR], brp[MAXDIR], bsp[MAXDIR], /* and the cross-terms */
btrace[MAXDIR], /* and the trace */
max_bval=0,
dcrush, dgss2, /* "delta" for crusher and gss2 gradients */
Dro, Dcrush, Dgss2; /* "DELTA" for readout, crusher and gss2 gradients */
/* Real-time variables used in this sequence **************/
int vpe_ctr = v1; // PE loop counter
int vpe_mult = v2; // PE multiplier, ranges from -PE/2 to PE/2
int vpe2_ctr = v3; // PE loop counter
int vpe2_mult = v4; // PE multiplier, ranges from -PE/2 to PE/2
int vpe2_offset = v5;
int vpe2_steps = v6;
int vms_slices = v7; // Number of slices
int vms_ctr = v8; // Slice loop counter
int vseg = v9; // Number of ETL segments
int vseg_ctr = v10; // Segment counter
int vetl = v11; // Echo train length
int vetl_ctr = v12; // Echo train loop counter
int vssc = v13; // Compressed steady-states
int vtrimage = v14; // Counts down from nt, trimage delay when 0
int vacquire = v15; // Argument for setacqvar, to skip steady state acquires
int vphase180 = v16; // phase of 180 degree refocusing pulse
int vetl_loop = v17; // Echo train length MINUS ONE, used on etl loop
int vnav = v18; // Echo train length
int vcr_ctr = v19; // variable crusher, index into table
int vcr1 = v20; // multiplier along RO
int vcr2 = v21; // multiplier along PE
int vcr3 = v22; // multiplier along SL
int vetl1 = v23; // = etl-1, determine navigator echo location in echo loop
int vcr_reset = v24; // check for navigator echoes, reset crushers
/* Initialize paramaters **********************************/
get_parameters();
te1 = getval("te1"); /* te1 is the echo time for the first echo */
cscale = getval("cscale"); /* Scaling factor on first 180 crushers */
vcrush = getval("vcrush"); /* Variable crusher or set amplitude? */
getstr("diffpat",diffpat);
/* Load external PE table ********************************/
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
} else {
abort_message("petable undefined");
}
/* Hold variable crushers in tables 5, 6, 7 */
settable(t5,8,crro);
settable(t6,8,crpe);
settable(t7,8,crss);
seqtime = 0.0;
espmin = 0.0;
/* RF Power & Bandwidth Calculations **********************/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
init_rf(&p2_rf,p2pat,p2,flip2,rof1,rof2);
// shape_rf(&p1_rf,"p1",p1pat,p1,flip1,rof1,rof2);
// shape_rf(&p2_rf,"p2",p2pat,p2,flip2,rof1,rof2);
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
/* Initialize gradient structures *************************/
init_readout(&ro_grad,"ro",lro,np,sw);
init_readout_refocus(&ror_grad,"ror");
init_phase(&pe_grad,"pe",lpe,nv);
init_phase(&pe2_grad,"pe2",lpe2,nv2);
init_slice(&ss_grad,"ss",thk); /* NOTE assume same band widths for p1 and p2 */
init_slice(&ss2_grad,"ss2",thk); /* not butterfly, want to scale crushers w/ echo */
init_slice_refocus(&ssr_grad,"ssr");
/* Gradient calculations **********************************/
calc_readout(&ro_grad,WRITE,"gro","sw","at");
calc_readout_refocus(&ror_grad,&ro_grad,NOWRITE,"gror");
calc_phase(&pe_grad,NOWRITE,"gpe","tpe");
calc_phase(&pe2_grad,NOWRITE,"gpe2","tpe2");
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice(&ss2_grad,&p1_rf,WRITE,"");
calc_slice_refocus(&ssr_grad,&ss_grad,WRITE,"gssr");
/* Equalize refocus and PE gradient durations *************/
calc_sim_gradient(&ror_grad,&pe_grad,&pe2_grad,0.0,WRITE);
/* Variable crusher */
init_generic(&crush_grad,"crush",gcrush,tcrush);
calc_generic(&crush_grad,WRITE,"","");
/* Create optional prepulse events ************************/
if (sat[0] == 'y') create_satbands();
if (fsat[0] == 'y') create_fatsat();
if (mt[0] == 'y') create_mtc();
/* Optional Diffusion gradient */
if (diff[0] == 'y') {
init_generic(&diff_grad,"diff",gdiff,tdelta);
if (!strcmp("sine",diffpat)) {
diff_grad.shape = SINE;
diffamp = gdiff*1;
}
/* adjust duration, so tdelta is from start ramp up to start ramp down */
if ((ix == 1) && (diff_grad.shape == TRAPEZOID)) {
calc_generic(&diff_grad,NOWRITE,"","");
diff_grad.duration += diff_grad.tramp;
}
calc_generic(&diff_grad,WRITE,"","");
}
/* Set up frequency offset pulse shape list ********/
offsetlist(pss,ss_grad.amp,0,freq90,ns,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shapelist90 = shapelist(p1_rf.pulseName,ss_grad.rfDuration, freq90, ns,0,seqcon[1]);
shapelist180 = shapelist(p2_rf.pulseName,ss2_grad.rfDuration,freq180,ns,0,seqcon[1]);
/* same slice selection gradient and RF pattern used */
if (ss_grad.rfFraction != 0.5)
abort_message("RF pulse must be symmetric (RF fraction = %.2f)",ss_grad.rfFraction);
if (ro_grad.echoFraction != 1)
abort_message("Echo Fraction must be 1");
/*****************************************************/
/* TIMING FOR ECHOES *********************************/
/*****************************************************/
/* First echo time, without diffusion */
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront;
tau2 = ss2_grad.rfCenterBack + crush_grad.duration + pe_grad.duration + ro_grad.timeToEcho;
te1min = 2*MAX(tau1,tau2);
if (te1 < te1min + 2*4e-6) {
abort_message("First echo time too small, minimum is %.2fms\n",(te1min+2*4e-6)*1000);
}
/* Each half-echo period in the ETL loop ********/
tau3 = ro_grad.timeFromEcho + pe_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront;
espmin = 2*MAX(tau2,tau3); // Minimum echo spacing
if (minesp[0] == 'y') {
esp = espmin + 2*4e-6;
putvalue("esp",esp);
}
if (esp - (espmin + 2*4e-6) < -12.5e-9) {
abort_message("Echo spacing too small, minimum is %.2fms\n",(espmin+2*4e-6)*1000);
}
te1_delay = te1/2.0 - tau1;
te2_delay = esp/2.0 - tau2;
te3_delay = esp/2.0 - tau3;
/*****************************************************/
/* TIMING FOR DIFFUSION ******************************/
/*****************************************************/
del1 = te1/2.0 - tau1;
del2 = 0;
del3 = te1/2.0 - tau2;
del4 = 0;
if (diff[0] == 'y') {
tau1 += diff_grad.duration;
tau2 += diff_grad.duration;
te1min = 2*MAX(tau1,tau2);
if (te1 < te1min + 4*4e-6) { /* te1 is split into 4 delays, each of which must be >= 4us */
abort_message("ERROR %s: First echo time too small, minimum is %.2fms\n",seqfil,te1min*1000);
}
/* te1 is the echo time for the first echo */
te_diff1 = te1/2 - tau1; /* Available time in first half of first echo */
te_diff2 = te1/2 - tau2; /* Available time in second half of first echo */
tmp1 = ss2_grad.duration + 2*crush_grad.duration; /* duration of 180 block */
/* Is tDELTA long enough? */
if (tDELTA < diff_grad.duration + tmp1)
abort_message("DELTA too short, increase to %.2fms",
(diff_grad.duration + tmp1)*1000);
/* Is tDELTA too long? */
tmp2 = diff_grad.duration + te_diff1 + tmp1 + te_diff2;
if (tDELTA > tmp2) {
abort_message("DELTA too long, increase te1 to %.2fms",
(te1 + (tDELTA-tmp2))*1000);
}
/* First attempt to put lobes right after slice select, ie del1 = 0 */
del1 = 4e-6; /* At least 4us after setting power for 180 */
del2 = te_diff1 - del1;
del3 = tDELTA - (diff_grad.duration + del2 + tmp1);
if (del3 < 4e-6) { /* shift diffusion block towards acquisition */
del3 = 4e-6;
del2 = tDELTA - (diff_grad.duration + tmp1 + del3);
}
del1 = te_diff1 - del2;
del4 = te_diff2 - del3;
if (fabs(del4) < 12.5e-9) del4 = 0;
}
te = te1 + (kzero-1)*esp; // Return effective TE
putvalue("te",te);
/* How many echoes in the echo loop, including navigators? */
etlnav = (etl-1)+(navigator[0]=='y')*2.0;
/* Minimum TR **************************************/
seqtime = 4e-6 + 2*nseg*ns*4e-6; /* count all the 4us delays */
seqtime += ns*(ss_grad.duration/2 + te1 + (etlnav)*esp + ro_grad.timeFromEcho + pe_grad.duration + te3_delay);
/* Increase TR if any options are selected****************/
if (sat[0] == 'y') seqtime += ns*satTime;
if (fsat[0] == 'y') seqtime += ns*fsatTime;
if (mt[0] == 'y') seqtime += ns*mtTime;
trmin = seqtime + ns*4e-6; /* Add 4us to ensure that tr_delay is always >= 4us */
if (mintr[0] == 'y'){
tr = trmin;
putvalue("tr",tr+1e-6);
}
if (tr < trmin) {
abort_message("TR too short. Minimum TR = %.2fms\n",trmin*1000);
}
tr_delay = (tr - seqtime)/ns;
/* Set number of segments for profile or full image **********/
nseg = prep_profile(profile[0],nv/etl,&pe_grad,&per_grad);
pe2_steps = prep_profile(profile[1],nv2,&pe2_grad,&pe2r_grad);
/* Calculate total scan time */
g_setExpTime(tr*(nt*nseg*pe2_steps*arraydim + ssc));
/***************************************************/
/* CALCULATE B VALUES ******************************/
if (diff[0] == 'y') {
/* Get multiplication factors and make sure they have same # elements */
/* All this is only necessary because putCmd only work for ix==1 */
nbro = (int) getarray("dro",roarr); nbval = nbro;
nbpe = (int) getarray("dpe",pearr); if (nbpe > nbval) nbval = nbpe;
nbsl = (int) getarray("dsl",slarr); if (nbsl > nbval) nbval = nbsl;
if ((nbro != nbval) && (nbro != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (readout)",seqfil);
if ((nbpe != nbval) && (nbpe != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (phase)",seqfil);
if ((nbsl != nbval) && (nbsl != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (slice)",seqfil);
if (nbro == 1) for (i = 1; i < nbval; i++) roarr[i] = roarr[0];
if (nbpe == 1) for (i = 1; i < nbval; i++) pearr[i] = pearr[0];
if (nbsl == 1) for (i = 1; i < nbval; i++) slarr[i] = slarr[0];
}
else {
nbval = 1;
roarr[0] = 0;
pearr[0] = 0;
slarr[0] = 0;
}
for (i = 0; i < nbval; i++) {
dcrush = crush_grad.duration; //"delta" for crusher
Dcrush = dcrush + ss_grad.duration; //"DELTA" for crusher
/* Readout */
Dro = ror_grad.duration;
bro[i] = bval(gdiff*roarr[i],tdelta,tDELTA);
bro[i] += bval(ro_grad.amp,ro_grad.timeToEcho,Dro);
bro[i] += bval(crush_grad.amp,dcrush,Dcrush);
bro[i] += bval_nested(gdiff*roarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
/* Slice */
dgss2 = Dgss2 = ss_grad.rfCenterFront;
bsl[i] = bval(gdiff*slarr[i],tdelta,tDELTA);
bsl[i] += bval(crush_grad.amp,dcrush,Dcrush);
bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval_nested(ss2_grad.ssamp,dgss2,Dgss2,
crush_grad.amp,dcrush,Dcrush);
/* Phase */
bpe[i] = bval(gdiff*pearr[i],tdelta,tDELTA);
bpe[i] += bval(crush_grad.amp,dcrush,Dcrush);
bpe[i] += bval_nested(gdiff*pearr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
/* Readout/Slice Cross-terms */
brs[i] = bval2(gdiff*roarr[i],gdiff*slarr[i],tdelta,tDELTA);
brs[i] += bval2(crush_grad.amp,
crush_grad.amp,dcrush,Dcrush);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
brs[i] += bval_cross(gdiff*slarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,
ss2_grad.ssamp,dgss2,Dgss2);
brs[i] += bval_cross(crush_grad.amp,dcrush,Dcrush,
ss2_grad.ssamp,dgss2,Dgss2);
/* Readout/Phase Cross-terms */
brp[i] = bval2(gdiff*roarr[i],gdiff*pearr[i],tdelta,tDELTA);
brp[i] += bval2(crush_grad.amp,
crush_grad.amp,dcrush,Dcrush);
brp[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
brp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
/* Slice/Phase Cross-terms */
bsp[i] = bval2(gdiff*pearr[i],gdiff*slarr[i],tdelta,tDELTA);
bsp[i] += bval2(crush_grad.amp,
crush_grad.amp,dcrush,Dcrush);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
bsp[i] += bval_cross(gdiff*slarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,
ss2_grad.ssamp,dgss2,Dgss2);
bsp[i] += bval_cross(crush_grad.amp,dcrush,Dcrush,
ss2_grad.ssamp,dgss2,Dgss2);
btrace[i] = (bro[i]+bsl[i]+bpe[i]);
if (max_bval < btrace[i]) {
max_bval = (bro[i]+bsl[i]+bpe[i]);
}
} /* End for-all-directions */
putarray("bvalrr",bro,nbval);
putarray("bvalpp",bpe,nbval);
putarray("bvalss",bsl,nbval);
putarray("bvalrp",brp,nbval);
putarray("bvalrs",brs,nbval);
putarray("bvalsp",bsp,nbval);
putarray("bvalue",btrace,nbval);
putvalue("max_bval",max_bval);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* PULSE SEQUENCE *************************************/
if (ix == 1) grad_advance(tep);
initval(fabs(ssc),vssc); // Compressed steady-state counter
setacqvar(vacquire); // Control acquisition through vacquire
assign(one,vacquire); // Turn on acquire when vacquire is zero
/* Phase cycle: Alternate 180 phase to cancel residual FID */
mod2(ct,vphase180); // 0101
dbl(vphase180,vphase180); // 0202
add(vphase180,one,vphase180); // 1313 Phase difference from 90
add(vphase180,oph,vphase180);
obsoffset(resto);
delay(4e-6);
initval(nseg,vseg);
initval(pe2_steps/2.0,vpe2_offset);
initval(etl,vetl);
initval(etl-1,vetl1);
peloop2(seqcon[3],pe2_steps,vpe2_steps,vpe2_ctr);
/* Use standard encoding order for 2nd PE dimension */
sub(vpe2_ctr,vpe2_offset,vpe2_mult);
loop(vseg,vseg_ctr);
/* Compressed steady-states: 1st array & transient, all arrays if ssc is negative */
if ((ix > 1) && (ssc > 0))
assign(zero,vssc);
sub(vseg_ctr,vssc,vseg_ctr); // vpe_ctr counts up from -ssc
assign(zero,vssc);
ifzero(vseg_ctr);
assign(zero,vacquire); // Start acquiring when vseg_ctr reaches zero
endif(vseg_ctr);
msloop(seqcon[1],ns,vms_slices,vms_ctr);
if (ticks) {
xgate(ticks);
grad_advance(tep);
}
sp1on(); delay(4e-6); sp1off(); // Scope trigger
/* Prepulse options ***********************************/
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
/* 90 degree pulse ************************************/
rotate();
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shapelist90,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Read dephase and Slice refocus *********************/
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0.0,0.0,-ssr_grad.amp,WAIT);
/* First half-TE delay ********************************/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(del1);
/* DIFFUSION GRADIENT */
if (diff[0] == 'y')
obl_shapedgradient(diff_grad.name,diff_grad.duration,diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
delay(del2);
/*****************************************************/
/* FIRST ECHO OUTSIDE LOOP ***************************/
/*****************************************************/
ifzero(vacquire); // real acquisition, get PE multiplier from table
mult(vseg_ctr,vetl,vpe_ctr);
getelem(t1,vpe_ctr,vpe_mult);
elsenz(vacquire); // steady state scan
assign(zero,vpe_mult);
endif(vacquire);
/* Variable crusher */
assign(zero,vcr_ctr);
getelem(t5,vcr_ctr,vcr1);
getelem(t6,vcr_ctr,vcr2);
getelem(t7,vcr_ctr,vcr3);
if(vcrush)
phase_encode3_oblshapedgradient(crush_grad.name,crush_grad.name,crush_grad.name,
crush_grad.duration,
(double)0,(double)0,(double)0, // base levels
crush_grad.amp*cscale,crush_grad.amp*cscale,crush_grad.amp*cscale, // step size
vcr1,vcr2,vcr3, // multipliers
(double)1.0,(double)1.0,(double)1.0, // upper limit on multipliers
1,WAIT,0);
else
obl_shapedgradient(crush_grad.name,crush_grad.duration,
crush_grad.amp,crush_grad.amp,crush_grad.amp,WAIT);
/* 180 degree pulse *******************************/
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shapelist180,ss2_grad.rfDuration,vphase180,rof1,rof2,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
if (vcrush)
phase_encode3_oblshapedgradient(crush_grad.name,crush_grad.name,crush_grad.name,
crush_grad.duration,
(double)0,(double)0,(double)0, // base levels
crush_grad.amp*cscale,crush_grad.amp*cscale,crush_grad.amp*cscale, // step size
vcr1,vcr2,vcr3, // multipliers
(double)1.0,(double)1.0,(double)1.0, // upper limit on multipliers
1,WAIT,0);
else
obl_shapedgradient(crush_grad.name,crush_grad.duration,
crush_grad.amp,crush_grad.amp,crush_grad.amp,WAIT);
delay(del3);
/* DIFFUSION GRADIENT */
if (diff[0] == 'y')
obl_shapedgradient(diff_grad.name,diff_grad.duration,diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
delay(del4);
/* Phase-encode gradient ******************************/
pe2_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp,0,0,
-pe_grad.increment,-pe2_grad.increment,vpe_mult,vpe2_mult,WAIT);
/* Readout gradient ************************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.roamp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
/* Acquire data ****************************************/
startacq(10e-6);
acquire(np,1.0/sw);
endacq();
delay(ro_grad.atDelayBack);
/* Rewinding phase-encode gradient ********************/
pe2_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,
pe_grad.increment,pe2_grad.increment,vpe_mult,vpe2_mult,WAIT);
/* Second half-TE delay *******************************/
delay(te3_delay);
/*****************************************************/
/* LOOP THROUGH THE REST OF ETL **********************/
/*****************************************************/
peloop(seqcon[2],etlnav,vetl_loop,vetl_ctr);
ifzero(vacquire); // real acquisition, get PE multiplier from table
mult(vseg_ctr,vetl,vpe_ctr);
add(vpe_ctr,vetl_ctr,vpe_ctr);
add(vpe_ctr,one,vpe_ctr);
getelem(t1,vpe_ctr,vpe_mult);
elsenz(vacquire); // steady state scan
assign(zero,vpe_mult);
endif(vacquire);
/* But don't phase encode navigator echoes */
ifrtGE(vetl_ctr,vetl1,vnav);
assign(zero,vpe_mult);
endif(vnav);
/* Variable crusher */
incr(vcr_ctr); /* Get next crusher level */
/* Except if we're doing navigators, start over */
sub(vetl1,vetl_ctr,vcr_reset);
ifzero(vcr_reset);
assign(zero,vcr_ctr);
endif(vcr_reset);
getelem(t5,vcr_ctr,vcr1);
getelem(t6,vcr_ctr,vcr2);
getelem(t7,vcr_ctr,vcr3);
phase_encode3_oblshapedgradient(crush_grad.name,crush_grad.name,crush_grad.name,
crush_grad.duration,
(double)0,(double)0,(double)0, // base levels
crush_grad.amp,crush_grad.amp,crush_grad.amp, // step size
vcr1,vcr2,vcr3, // multipliers
(double)1.0,(double)1.0,(double)1.0, // upper limit on multipliers
1,WAIT,0);
/* 180 degree pulse *******************************/
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shapelist180,ss2_grad.rfDuration,vphase180,rof1,rof2,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
/* Variable crusher */
phase_encode3_oblshapedgradient(crush_grad.name,crush_grad.name,crush_grad.name,
crush_grad.duration,
(double)0,(double)0,(double)0, // base levels
crush_grad.amp,crush_grad.amp,crush_grad.amp, // step size
vcr1,vcr2,vcr3, // multipliers
(double)1.0,(double)1.0,(double)1.0, // upper limit on multipliers
1,WAIT,0);
/* Phase-encode gradient ******************************/
pe2_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,
-pe_grad.increment,-pe2_grad.increment,vpe_mult,vpe2_mult,WAIT);
/* Second half-TE period ******************************/
delay(te2_delay);
/* Readout gradient ************************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.roamp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(10e-6);
acquire(np,1.0/sw);
endacq();
delay(ro_grad.atDelayBack);
/* Rewinding phase-encode gradient ********************/
pe2_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,
pe_grad.increment,pe2_grad.increment,vpe_mult,vpe2_mult,WAIT);
/* Second half-TE delay *******************************/
delay(te3_delay);
endpeloop(seqcon[2],vetl_ctr);
/* Relaxation delay ***********************************/
if (!trtype)
delay(tr_delay);
endmsloop(seqcon[1],vms_ctr);
if (trtype)
delay(ns*tr_delay);
endloop(vseg_ctr);
endpeloop(seqcon[3],vpe2_ctr);
/* Inter-image delay **********************************/
sub(ntrt,ct,vtrimage);
decr(vtrimage);
ifzero(vtrimage);
delay(trimage);
endif(vtrimage);
}
pulsesequence()
{
/* Internal variable declarations *********************/
char txphase[MAXSTR];
char rxphase[MAXSTR];
char my_p1pat[MAXSTR];
char my_p4pat[MAXSTR];
char my_p2pat[MAXSTR];
char my_p3pat[MAXSTR];
char blankmode[MAXSTR]={0};
char tmpstr[MAXSTR];
double postDelay;
double rfDuration;
double acqt;
int i,ret=-1;
static int phs1[4] = {0,2,1,3}; /* from T1meas.c */
int my_pulseID;
double my_offsets[64];
double my_tpwr[64];
double my_tpwrf[64];
int my_on_off[64];
double mytmp;
int my_numrfch;
int my_retval;
for(i=0;i<64;i++) my_offsets[i] = 0.0;
/*************************************************/
/* Initialize paramter **************************/
i = 0;
postDelay = 0.5;
acqt = 0.0;
// getstr("rxphase",rxphase);
// getstr("txphase",txphase);
getstr("p1pat",my_p1pat);
getstr("p2pat",my_p2pat);
getstr("p3pat",my_p3pat);
getstr("p4pat",my_p4pat);
ret = P_getstring(GLOBAL,"blankmode",blankmode,1,MAXSTR);
if ( P_getreal(CURRENT,"ampargs",&mytmp,2) < 0 )
mytmp = 0.0;
if ( P_getreal(GLOBAL, "numrfch", &mytmp, 1) < 0 )
abort_message("Cannot proceed without global numrfch\n");
my_numrfch = (int)(mytmp+0.05);
if(my_numrfch<2) abort_message("this is a single transmit system and you don't need this pulse sequence\n");
if(my_numrfch>16) abort_message("numrfch > 16 not supported \n");
printf("mytmp=%f\n",mytmp);
// if((P_getstring(GLOBAL,"rfGroupMap",tmpstr,1,MAXSTR) < 0) || (strlen(tmp) < 2))
// {
// abort_message("global rfGroupMap doesn't exist or is too short\n");
// }
// else // rfGroupMap is set to all 1's for the same number as numrfch so we control everything here in the sequence
//{
strncpy(tmpstr,"111111111111111111111111111111111111111111111111111111111111111111",(size_t)my_numrfch);
tmpstr[my_numrfch]=0;
P_setstring(CURRENT, "rfGroupMap", tmpstr, 1);
// }
//getparm("blankmode","string",GLOBAL,blankmode,MAXSTR);
postDelay = tr - at;
//printf("blankmode=%s\n",blankmode);
/*************************************************/
/* check phase setting ***************************/
// if ( (txphase[0] =='n') && (rxphase[0] =='n') )
// {
// abort_message("ERROR - Select at least one phase [Tx or Rx]\n");
// }
/**************************************************/
/* check pulse width *****************************/
rfDuration = shapelistpw(p1pat, pw); /* assign exitation pulse duration */
printf("p1pat: %s\n",my_p1pat);
printf("duration: %e\n",rfDuration);
acqt = rfDuration + rof1 - alfa;
if (FP_GT(acqt, at))
{
abort_message("Pulse duration too long. max [%.3f] ms\n",(at-rof1+alfa)*1000.0);
}
if(ret==0 && blankmode[0]=='u')
obsunblank();
delay(postDelay);
settable(t1,4,phs1); /*from T1meas.c */
getelem(t1,ct,v11); /*from T1meas.c */
setreceiver(t1);
printf("mytmp=%d\n",my_numrfch);
my_pulseID = initRFGroupPulse(rfDuration, my_p1pat, 's', 0.0, 0.0, v11, &my_offsets[0], my_numrfch-1);
printf("pulse id = %d\n",my_pulseID);
//modifyRFGroupName(my_pulseID,2,my_p2pat);
//modifyRFGroupName(my_pulseID,3,my_p3pat);
// modifyRFGroupName(my_pulseID,4,my_p4pat);
for(i=0;i<64;i++) my_tpwr[i]=0.0;
for(i=0;i<64;i++) my_tpwrf[i]=0.0;
for(i=0;i<64;i++) my_on_off[i]=0;
//SAS turn everything off
for(i=0;i<my_numrfch-1;i++)
{
modifyRFGroupOnOff(my_pulseID, i+1,0);
printf("here is i=%d\n",i);
}
for(i=0;i<my_numrfch-1;i++) modifyRFGroupPwrf(my_pulseID, i+1, 0.0);
for(i=0;i<my_numrfch-1;i++) modifyRFGroupPwrC(my_pulseID, i+1, 0.0);
//SAS get the parameter arrays into the local arrays
my_retval=(int)getarray("my_tpwr",my_tpwr);
/*
printf("my tpwr0 was: %e\n",my_tpwr[0]);
printf("my tpwr1 was: %e\n",my_tpwr[1]);
printf("my tpwr2 was: %e\n",my_tpwr[2]);
printf("my tpwr3 was: %e\n",my_tpwr[3]);
printf("my tpwr4 was: %e\n",my_tpwr[4]);
printf("my tpwr5 was: %e\n",my_tpwr[5]);
printf("my tpwr6 was: %e\n",my_tpwr[6]);
printf("my tpwr7 was: %e\n",my_tpwr[7]);
*/
my_retval=(int)getarray("my_on_off",my_tpwrf); //dump the array of reals into a real array
for(i=0;i<my_numrfch;i++) my_on_off[i] = (int)my_tpwrf[i]; //convert to integer
/*
printf("my on_off_0 was: %d\n",my_on_off[0]);
printf("my on_off_1 was: %d\n",my_on_off[1]);
printf("my on_off_2 was: %d\n",my_on_off[2]);
printf("my on_off_3 was: %d\n",my_on_off[3]);
printf("my on_off_4 was: %d\n",my_on_off[4]);
printf("my on_off_5 was: %d\n",my_on_off[5]);
printf("my on_off_6 was: %d\n",my_on_off[6]);
printf("my on_off_7 was: %d\n",my_on_off[7]);
*/
for(i=0;i<64;i++) my_tpwrf[i]=2047.0;
//SAS set everything to array values
for(i=0;i<my_numrfch;i++) modifyRFGroupOnOff(my_pulseID, i+1,my_on_off[i]);
for(i=0;i<my_numrfch;i++) modifyRFGroupPwrf(my_pulseID, i+1, my_tpwrf[i]);
for(i=0;i<my_numrfch;i++) modifyRFGroupPwrC(my_pulseID, i+1, my_tpwr[i]);
/*==============================================*/
/* START LOOPBACK PULSE SEQUENCE */
/*==============================================*/
status(A);
obsoffset(resto);
/* TTL trigger to scope sequence ****************************/
sp1on();
/* Relaxation delay ***********************************/
xgate(ticks);
/* RF pulse *******************************************/
GroupPulse(my_pulseID, rof1, rof2, v11, 0);
endacq();
sp1off();
if(ret==0 && blankmode[0]=='u')
obsunblank();
}
