void proj2D(struct data *d)
{
char seqcon[6];
/* For 2D projections we fake the data is 2D and recon accordingly */
/* Get the seqcon */
strcpy(seqcon,*sval("seqcon",&d->p));
/* ROxPE projection has profile='ny' */
if (spar(d,"profile","ny")) {
/* Adjust seqcon for 2D */
seqcon[3]='n';
setsval(&d->p,"seqcon",seqcon);
setseqmode(d);
default2D(d);
}
/* ROxPE2 projection has profile='yn' */
if (spar(d,"profile","yn")) {
/* Adjust seqcon for 2D */
seqcon[2]=seqcon[3];
seqcon[3]='n';
setsval(&d->p,"seqcon",seqcon);
setval(&d->p,"nv",d->nv2);
setval(&d->p,"nseg",d->nv2);
setval(&d->p,"etl",1);
setval(&d->p,"pelist",0);
setval(&d->p,"nv2",1);
setsval(&d->p,"apptype","im2D");
setdatapars(d);
setseqmode(d);
/* The following is required to be able to graphically plan on the output images:
thk = lpe
lpe = lpe2
ppe of each slice in turn = pss of each slice in turn
psi, phi, theta need to be corrected (90 degree rotation about readout axis)
*/
/* For now just adjust FOV and offset for centre of slice(s) */
setval(&d->p,"thk",*val("lpe",&d->p));
setval(&d->p,"lpe",*val("lpe2",&d->p));
setval(&d->p,"ppe",*val("pss0",&d->p));
default2D(d);
}
}
void defaultEPI(struct data *d)
{
int DISCARD=-1;
int refEPI=FALSE,refSGE=FALSE;
int getscaleref=FALSE;
double oversample,lro,lpe;
struct data ref1,ref2,ref3,ref4,ref5,ref6;
struct segscale scale1,scale2;
enum {
OFF = 0,
POINTWISE = 1,
TRIPLE = 2,
SCALED_TRIPLE = 3
} epi_pc;
#ifdef DEBUG
char function[20];
strcpy(function,"defaultEPI"); /* Set function name */
#endif
/* Set EPI correction scheme */
if (spar(d,"epi_pc","POINTWISE")) epi_pc=POINTWISE;
else if (spar(d,"epi_pc","TRIPLE")) epi_pc=TRIPLE;
else if (spar(d,"epi_pc","SCALED_TRIPLE")) epi_pc=SCALED_TRIPLE;
else epi_pc=OFF;
/* Check whether to output or discard reference scans */
if (spar(d,"imRF","y")) refEPI=TRUE;
if (spar(d,"imSGE","y")) refSGE=TRUE;
/* Set reference data */
if (epi_pc > OFF) { /* Pointwise or triple reference phase correction */
getpars(d->procpar,&ref1);
initdata(&ref1);
getpars(d->procpar,&ref3); /* ref3 used in pointwise phase correction of inverted */
initdata(&ref3); /* reference scans if reference output is selected */
}
if (epi_pc > POINTWISE) { /* Triple reference phase corrections */
getpars(d->procpar,&ref2);
initdata(&ref2);
getpars(d->procpar,&ref4);
initdata(&ref4);
}
if (epi_pc > TRIPLE) { /* Scaled triple reference phase correction */
getpars(d->procpar,&ref5);
initdata(&ref5);
getpars(d->procpar,&ref6);
initdata(&ref6);
}
d->nv=(int)*val("nphase",&d->p); /* Set d->nv for dimorder2D */
d->pssorder=sliceorder(d,d->ns,"pss"); /* Fill pssorder with the slice order */
d->dim2order=phaseorder(d,d->nv,"par_does_not_exist"); /* Set dim2order=-1 for sequential phase encode order */
d->dim3order=phaseorder(d,d->nv,"sgepelist"); /* Fill dim3order with the standard gradient echo phase encode order */
d->nv2=d->nv; /* Set d->nv2 for dim3order */
d->dimorder=IM2D; /* Set dimorder flag */
d->nv=(int)*val("nseg",&d->p); /* Use d->nv for the number of shots */
setnvolsEPI(d); /* Set the number of data volumes */
/* Allow for scaled FOV in ASL test setup expt */
lro=*val("lro",&d->p)**val("aslfov",&d->p);
lpe=*val("lpe",&d->p)**val("aslfov",&d->p);
/* Set default of no compressed segment scaling just in case it's never set */
scale1.data=FALSE;
scale2.data=FALSE;
/* Loop over data blocks */
for (d->block=0;d->block<d->nblocks;d->block++) {
d->outvol=0; /* Initialise output data volume (that will not include reference scans) */
for (d->vol=0;d->vol<d->nvols;d->vol++) { /* Loop over "volumes" */
setoutvolEPI(d); /* Set output data volume */
if (d->outvol>d->endvol) break; /* Break if last requested volume has been processed */
getblockEPI(d,d->vol,NDCC); /* Get block without applying dbh.lvl and dbh.tlt */
zeromax(d); /* Zero max structure & coordinates of maximum */
zeronoise(d); /* Zero values in noise structure */
#ifdef DEBUG
fprintf(stdout,"\n%s: %s()\n",SOURCEFILE,function);
switch (epi_pc) {
case OFF: fprintf(stdout," Correction: OFF \n"); break;
case POINTWISE: fprintf(stdout," Correction: POINTWISE \n"); break;
case TRIPLE: fprintf(stdout," Correction: TRIPLE \n"); break;
case SCALED_TRIPLE: fprintf(stdout," Correction: SCALED_TRIPLE \n"); break;
}
fflush(stdout);
#endif
/* Process data as directed by image parameter */
switch ((int)getelem(d,"image",d->vol)) {
case 0: /* Reference, no phase-encode */
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (refEPI) w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
if (epi_pc > OFF) { /* If there is phase correction */
ftnpEPI(d); /* FT along readout dimension */
clear2Ddata(&ref1); /* Clear ref1 */
copy2Ddata(d,&ref1); /* Copy to ref1 */
ref1.datamode=EPIREF; /* Flag as EPIREF data */
} else { /* else there is no phase correction */
ref1.datamode=NONE; /* Flag as no data */
if (refEPI) ftnpEPI(d); /* FT along readout dimension */
}
setsegscale(d,&scale1); /* Set scaling for compressed segments */
segscale(d,&scale1); /* Scale compressed segments */
if (refEPI) /* If reference output is requested */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Else use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
case -1: /* Inverted Readout Reference, with phase-encode */
#ifdef DEBUG
fprintf(stdout," Processing reference -1 data ...\n");
fflush(stdout);
#endif
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (refEPI) w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
ftnpEPI(d); /* FT along readout dimension */
segscale(d,&scale2); /* Scale compressed segments */
if (epi_pc > POINTWISE) { /* if triple or scaled triple reference phase correction */
clear2Ddata(&ref2); /* Clear ref2 */
copy2Ddata(d,&ref2); /* Copy to ref2 */
ref2.datamode=EPIREF; /* Flag ref2 as EPIREF data */
if (ref3.datamode == EPIREF) { /* if there is ref3 reference data */
phaseEPIref(&ref2,&ref3,&ref4); /* Phase correct ref2 data using ref3 and put result in ref4 */
/* analyseEPInav(&ref4); // Analyse the navigators */
stripEPInav(&ref4); /* Strip the navigator scans */
ftnvEPI(&ref4); /* FT along phase encode dimension */
revreadEPI(&ref4); /* Reverse the data in readout dimension */
getscaleref=TRUE; /* Flag to store the next regular image for scaling in SCALED_TRIPLE */
}
}
if (refEPI) { /* if reference output is requested */
if (ref3.datamode == EPIREF) { /* if there is ref3 reference data */
phaseEPI(d,&ref3); /* Phase correct with the reference */
}
navcorrEPI(d); /* Phase correct with the navigator */
stripEPInav(d); /* Strip the navigator scans */
ftnvEPI(d); /* FT along phase encode dimension */
revreadEPI(d); /* Reverse the data in readout dimension */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
}
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
case -2: /* Inverted Readout Reference, no phase-encode */
#ifdef DEBUG
fprintf(stdout," Processing reference -2 data ...\n");
fflush(stdout);
#endif
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (refEPI) w2Dfdfs(d,VJ,FLT32,d->vol);
ftnpEPI(d); /* FT along readout dimension */
setsegscale(d,&scale2); /* Set scaling for compressed segments */
segscale(d,&scale2); /* Scale compressed segments */
if (epi_pc > POINTWISE) { /* if old triple or triple reference phase correction */
clear2Ddata(&ref3); /* Clear ref3 */
copy2Ddata(d,&ref3); /* Copy to ref3 */
ref3.datamode=EPIREF; /* Flag ref3 as EPIREF data */
if (ref2.datamode == EPIREF) { /* if there is ref2 reference data */
phaseEPIref(&ref2,&ref3,&ref4); /* Phase correct ref2 data using ref3 and put result in ref4 */
/* analyseEPInav(&ref4); // Analyse the navigators */
stripEPInav(&ref4); /* Strip the navigator scans */
ftnvEPI(&ref4); /* FT along phase encode dimension */
revreadEPI(&ref4); /* Reverse the data in readout dimension */
getscaleref=TRUE; /* Flag to store the next regular image for scaling in SCALED_TRIPLE */
}
}
if (refEPI) { /* if reference output is requested */
if (epi_pc == POINTWISE) { /* if pointwise reference phase correction */
clear2Ddata(&ref3); /* Clear ref3 */
copy2Ddata(d,&ref3); /* Copy to ref3 */
ref3.datamode=EPIREF; /* Flag ref3 as EPIREF data */
}
revreadEPI(d); /* Reverse the data in readout dimension */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
}
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
case 1: /* Regular image */
#ifdef DEBUG
fprintf(stdout," Processing image 1 data ...\n");
fflush(stdout);
#endif
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (d->outvol>=d->startvol)
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
switch (epi_pc) {
case SCALED_TRIPLE: /* Scaled triple reference phase correction */
if (getscaleref) { /* If the scale reference has just been acquired */
clear2Ddata(&ref5); /* Clear ref5 */
copy2Ddata(d,&ref5); /* Copy to ref5 */
ref5.datamode=EPIREF; /* Flag ref5 as EPIREF data */
prepEPIref(&ref5,&ref1); /* Prepare ref5 data so it can be used to scale ref4 data */
}
break;
default:
break;
}
ftnpEPI(d); /* FT along readout dimension */
segscale(d,&scale1); /* Scale compressed segments */
phaseEPI(d,&ref1); /* Phase correct with the reference */
navcorrEPI(d); /* Phase correct with the navigator */
/* analyseEPInav(d); // Analyse the navigators */
stripEPInav(d); /* Strip the navigator scans */
ftnvEPI(d); /* FT along phase encode dimension */
switch (epi_pc) {
case TRIPLE: /* Triple reference phase correction */
addEPIref(d,&ref4); /* Add ref4 data to cancel N/2 ghost */
break;
case SCALED_TRIPLE: /* Scaled triple reference phase correction */
if (getscaleref) { /* If the scale reference has just been acquired */
addEPIref(d,&ref4); /* Add ref4 data to cancel N/2 ghost */
getscaleref=FALSE; /* Flag that scale reference has been acquired */
} else {
addscaledEPIref(d,&ref4,&ref5); /* Scale ref4 data according to d/ref5, then add to d */
}
break;
default:
break;
}
if (d->outvol>=d->startvol) {
phasedata2D(d,VJ); /* Phase data if required */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Write 2D fdf data from volume */
wnifti(d,VJ,FLT32,d->vol);
}
break;
default: /* Reference Standard Gradient Echo */
setblockSGE(d);
setval(&d->p,"lro",lro); /* Set suitable lro in case it has been scaled */
setval(&d->p,"lpe",lpe); /* Set suitable lpe in case it has been scaled */
if (refSGE) w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
getmax(d); /* Get coordinates of maximum */
shiftdata2D(d,OPT); /* Shift FID data for fft */
equalizenoise2D(d,STD); /* Scale for equal noise in all receivers */
phaseramp2D(d,READ); /* Phase ramp the data to correct for readout offset pro */
phaseramp2D(d,PHASE); /* Phase ramp the data to correct for phase encode offset ppe */
weightdata2D(d,STD); /* Weight data using standard VnmrJ parameters */
oversample=*val("oversample",&d->p); /* Check to see if there is oversampling */
d->fn *=oversample; /* Correct d->fn for oversample */
zerofill2D(d,STD); /* Zero fill data using standard VnmrJ parameters */
fft2D(d); /* 2D fft */
phasedata2D(d,VJ); /* Phase data if required */
shiftdata2D(d,STD); /* Shift data to get images */
if (oversample>1) zoomEPI(d); /* If oversampled, zoom to get the requested FOV */
if (refSGE) /* If standard gradient echo reference output is requested */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Else use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
} /* end image parameter switch */
clear2Ddata(d); /* Clear data volume from memory */
setdatapars(d); /* Sets d->nv=1 */
d->nv=*val("nseg",&d->p); /* Use d->nv for the number of shots */
d->nv2=(int)*val("nphase",&d->p); /* Use d->nv2 for number of standard gradient echo phase encodes */
d->zerofill=FALSE; /* Make sure setdatapars will not overwrite d->nv */
} /* end volume loop */
} /* end data block loop */
/* Clear all reference data */
if (epi_pc > OFF) { /* Pointwise or triple reference phase correction */
clear2Dall(&ref1);
clear2Dall(&ref3);
}
if (epi_pc > POINTWISE) { /* Triple and scaled triple reference phase correction */
clear2Dall(&ref2);
clear2Dall(&ref4);
}
if (epi_pc > TRIPLE) { /* Scaled triple reference phase correction */
clear2Dall(&ref5);
clear2Dall(&ref6);
}
clear2Dall(d); /* Clear everything from memory */
}
