-
Notifications
You must be signed in to change notification settings - Fork 0
/
hmri_create_b1map.m
702 lines (579 loc) · 29.5 KB
/
hmri_create_b1map.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
function P_trans = hmri_create_b1map(jobsubj)
%% Processing of B1 maps for B1 bias correction
% FORMAT P_trans = hmri_create_b1map(jobsubj)
% jobsubj - are parameters for one subject out of the job list.
% NB: ONE SINGLE DATA SET FROM ONE SINGLE SUBJECT IS PROCESSED HERE,
% LOOP OVER SUBJECTS DONE AT HIGHER LEVEL.
% P_trans - a vector of file names with P_trans(1,:) = anatomical volume
% for coregistration and P_trans(2,:) = B1 map in percent units.
%_______________________________________________________________________
% Written by E. Balteau, 2014.
% Cyclotron Research Centre, University of Liege, Belgium
%_______________________________________________________________________
% Modified by T. Leutritz in 2016 in order to use the SIEMENS product
% sequences 'rf_map' and 'tfl_b1map'. The latter produces essentially
% a FLASH like image and a flip angle map (multiplied by 10) based on
% Chung S. et al.: "Rapid B1+ Mapping Using a Preconditioning RF Pulse with
% TurboFLASH Readout", MRM 64:439-446 (2010).
%_______________________________________________________________________
% retrieve effective acquisition & processing parameters, alternatively
% use defaults
b1map_params = get_b1map_params(jobsubj);
% save b1map_params as json-file
spm_jsonwrite(fullfile(jobsubj.path.supplpath,'MPM_map_creation_b1map_params.json'),b1map_params,struct('indent','\t'));
% init output
P_trans = [];
% return if nothing else to be done (no B1 correction or UNICORT cases)
if ~b1map_params.b1avail
return;
end
% calculate B1 map according to b1 data type
switch(b1map_params.b1type)
case 'i3D_AFI'
% processing B1 map from AFI data
P_trans = calc_AFI_b1map(jobsubj, b1map_params);
case 'i3D_EPI'
% processing B1 map from SE/STE EPI data
P_trans = calc_SESTE_b1map(jobsubj, b1map_params);
case 'tfl_b1_map'
% processing B1 map from tfl_b1map data
P_trans = calc_tfl_b1map(jobsubj, b1map_params);
case 'rf_map'
% processing B1 map from rf_map data
P_trans = calc_rf_map(jobsubj, b1map_params);
case 'pre_processed_B1'
P_trans = b1map_params.b1input(1:2,:);
otherwise
fprintf('\nWARNING: unknown B1 type, no B1 map calculation performed.\n');
end
% copy P_trans output to Results/Supplementary directory (nii & json!) and
% make P_trans point to the copied files (so coregistration is applied to
% them).
%
% NOTES:
% - if "cleanup" set to true, the B1mapCalc directory is deleted when the
% Map Calculation completes...
% - just in case no json files have been saved with the output, the
% copyfile is called in "try" mode...
% - must strip the ',1' (at the end of the file extension '.nii,1')
% otherwise copyfile does not find the files!!
if ~isempty(P_trans)
P_trans = spm_file(P_trans,'number','');
P_trans_copy{1} = fullfile(jobsubj.path.supplpath, spm_file(P_trans(1,:), 'filename'));
P_trans_copy{2} = fullfile(jobsubj.path.supplpath, spm_file(P_trans(2,:), 'filename'));
copyfile(deblank(P_trans(1,:)), P_trans_copy{1});
try copyfile([spm_str_manip(P_trans(1,:),'r') '.json'],[spm_str_manip(P_trans_copy{1},'r') '.json']); end %#ok<*TRYNC>
copyfile(deblank(P_trans(2,:)), P_trans_copy{2});
try copyfile([spm_str_manip(P_trans(2,:),'r') '.json'],[spm_str_manip(P_trans_copy{2},'r') '.json']); end
P_trans = char(P_trans_copy{1},P_trans_copy{2});
end
end
%% =======================================================================%
% B1 map calculation - AFI protocol
%=========================================================================%
function P_trans = calc_AFI_b1map(jobsubj, b1map_params)
% default format specifications for the output metadata
json = hmri_get_defaults('json');
% define output dir
outpath = jobsubj.path.b1path;
b1map_params.outpath = outpath;
% NB: both phase and magnitude images can be provided but only the
% magnitude images (first series) are used. Phase images (second series)
% are not used. In each series, first image = TR2 (long TR) and second
% image = TR1 (short TR).
fileTR1 = b1map_params.b1input(2,:);
fileTR2 = b1map_params.b1input(1,:);
V1 = spm_vol(fileTR1);
V2 = spm_vol(fileTR2);
Y1 = spm_read_vols(V1);
Y2 = spm_read_vols(V2);
TR1 = 1; % only the ratio [TR2/TR1=n] matters
TR2 = b1map_params.b1acq.TR2TR1ratio;
alphanom = b1map_params.b1acq.alphanom;
% Mask = squeeze(Vol1);
% threshold = (prctile(Mask(:),98)-prctile(Mask(:),2))*0.1+prctile(Mask(:),2);
% Mask = (Mask>threshold);
B1map = acos((Y2./Y1*TR2/TR1-1)./(TR2/TR1*ones(size(Y1))-Y2./Y1))*180/pi;
B1map_norm = abs(B1map)*100/alphanom;
% smoothed map
smB1map_norm = zeros(size(B1map_norm));
pxs = sqrt(sum(V1.mat(1:3,1:3).^2)); % Voxel resolution
smth = 8./pxs;
spm_smooth(B1map_norm,smB1map_norm,smth);
% masking
% B1map = B1map.*Mask;
% B1map_norm = B1map_norm.*Mask;
% smB1map_norm = smB1map_norm.*Mask;
sname = spm_file(V1.fname,'filename');
% save output images
VB1 = V1;
% VB1.pinfo = [max(B1map(:))/16384;0;0];
% VB1.fname = fullfile(outpath, [sname '_B1map.nii']);
% spm_write_vol(VB1,B1map);
% VB1.pinfo = [max(B1map_norm(:))/16384;0;0];
% VB1.fname = fullfile(outpath, [sname '_B1map_norm.nii']);
% spm_write_vol(VB1,B1map_norm);
VB1.pinfo = [max(smB1map_norm(:))/16384;0;0];
VB1.descrip = 'B1+ map - smoothed and normalised (p.u.) - AFI protocol';
VB1.fname = fullfile(outpath, [sname '_B1map.nii']);
spm_write_vol(VB1,smB1map_norm);
% set and write metadata
input_files = b1map_params.b1input;
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.output.imtype = 'B1+ map (AFI protocol)';
set_metadata(VB1.fname,Output_hdr,json);
% Rename anatomical reference for uniformity between protocols
B1ref = fullfile(outpath, [sname '_B1ref.nii']);
copyfile(char(fileTR1),B1ref);
try copyfile([spm_str_manip(char(fileTR1),'r') '.json'],[spm_str_manip(B1ref,'r') '.json']); end %#ok<*TRYNC>
% requires anatomic image + map
P_trans = char(B1ref,char(VB1.fname));
% VB1.fname = fullfile(outpath, [sname '_B1map_mask.nii']);
% spm_write_vol(VB1,Mask);
end
%% =======================================================================%
% B1 map calculation - SE/STE EPI protocol
%=========================================================================%
function P_trans = calc_SESTE_b1map(jobsubj, b1map_params)
% Calculation of B1 maps based on 3D EPI spin echo (SE) and stimulated
% (STE) echo images (see Jiru and Klose MRM 2006).
% Corresponding scanning protocol/sequence: al_B1mapping
% Input: 11 pairs of (SE, STE) images for B1 map calculation and 3 images
% for B0 map calculation.
% This macro calls the functions hmri_create_B1Map_unwarp and
% hmri_create_B1Map_process for correction of image distortions, padding
% and smoothing of the images.
% Output:
% - distorted B1 (B1map_*) and error (SDmap_*) maps
% - undistorted B1 (uB1map_*) and error (uSDmap_*) maps
% - undistorted, masked and padded B1 maps (muB1map_*)
% - undistorted, masked, padded and smoothed B1 maps (smuB1map_*)
% i.e. FULLY PROCESSED
% At each voxel, this macro selects the 5 pairs of (SE,STE image) (out of
% 11) with maximum signal amplitude in the SE images.
% The sum of square image of all SE images is created (SumOfSq) and
% undistorted (uSumOfSq) for coregistration of the B1 map to an anatomical
% dataset.
%
% For coherence among B1 protocols, the fully processed B1 map (smuB1map_*)
% is renamed *_B1map.nii, while the undistorted SoS image (uSumOfSq) is
% renamed *_B1ref for anatomical reference.
json = hmri_get_defaults('json');
P = b1map_params.b1input; % B1 data - 11 pairs
Q = b1map_params.b0input; % B0 data - 3 volumes
V = spm_vol(P);
n = numel(V);
Y_tmptmp = zeros([V(1).dim(1:2) n]);
Y_ab = zeros(V(1).dim(1:3));
Y_cd = zeros(V(1).dim(1:3));
Index_Matrix = zeros([V(1).dim(1:3) b1map_params.b1proc.Nonominalvalues]);
real_Y_tmp = zeros([V(1).dim(1:2) 2*b1map_params.b1proc.Nonominalvalues]);
Ssq_matrix = sqrt(sum(spm_read_vols(V(1:2:end)).^2,4));
%-Define output directory
%-----------------------------------------------------------------------
outpath = jobsubj.path.b1path;
b1map_params.outpath = outpath;
%-Start progress plot
%-----------------------------------------------------------------------
spm_progress_bar('Init',V(1).dim(3),'B1 map fit','planes completed');
%-Loop over planes computing result Y
%-----------------------------------------------------------------------
clear Temp_mat;
corr_fact = exp(b1map_params.b1acq.TM/b1map_params.b1proc.T1);
for p = 1:V(1).dim(3) %loop over the partition dimension of the data set
B = spm_matrix([0 0 -p 0 0 0 1 1 1]);
for i = 1:n/2
M = inv(B*inv(V(1).mat)*V(1).mat); %#ok<*MINV>
Y_tmptmp(:,:,((i-1)*2+1)) = real( ...
acos(corr_fact*spm_slice_vol(V((i-1)*2+2),M,V(1).dim(1:2),0) ./ ...
(spm_slice_vol(V((i-1)*2+1),M,V(1).dim(1:2),0)+b1map_params.b1proc.eps))/pi*180/b1map_params.b1acq.beta(i) ...
); % nearest neighbor interpolation
Y_tmptmp(:,:,((i-1)*2+2)) = 180/b1map_params.b1acq.beta(i) - Y_tmptmp(:,:,((i-1)*2+1));
Temp_mat(:,:,i) = spm_slice_vol(V((i-1)*2+1),M,V(1).dim(1:2),0); %#ok<*AGROW>
end
[~,indexes] = sort(Temp_mat,3);
for x_nr = 1:V(1).dim(1)
for y_nr = 1:V(1).dim(2)
for k=1:b1map_params.b1proc.Nonominalvalues
real_Y_tmp(x_nr,y_nr,2*k-1) = Y_tmptmp(x_nr,y_nr,2*indexes(x_nr,y_nr,n/2-k+1)-1);
real_Y_tmp(x_nr,y_nr,2*k) = Y_tmptmp(x_nr,y_nr,2*indexes(x_nr,y_nr,n/2-k+1));
Index_Matrix(x_nr,y_nr,p,k) = indexes(x_nr,y_nr,indexes(x_nr,y_nr,n/2-k+1));
end
end
end
Y_tmp = sort(real(real_Y_tmp), 3); % take the real value due to noise problems
Y_sd = zeros([V(1).dim(1:2) (b1map_params.b1proc.Nonominalvalues+1)]);
Y_mn = zeros([V(1).dim(1:2) (b1map_params.b1proc.Nonominalvalues+1)]);
for i = 1:(b1map_params.b1proc.Nonominalvalues+1)
Y_sd(:,:,i) = std(Y_tmp(:,:,i:(i + b1map_params.b1proc.Nonominalvalues-1)), [], 3);
Y_mn(:,:,i) = mean(Y_tmp(:,:,i:(i + b1map_params.b1proc.Nonominalvalues-1)), 3);
end
[~,min_index] = min(Y_sd,[],3); % !! min_index is a 2D array. Size given by resolution along read and phase directions
for x_nr = 1:V(1).dim(1)
for y_nr = 1:V(1).dim(2)
Y_ab(x_nr,y_nr,p) = Y_mn(x_nr,y_nr, min_index(x_nr,y_nr)); % Y_ab is the relative flip angle value averaged over the n flip angles (determined by minizing the SD i.e. keeping the most uniform relative flip angle values)
Y_cd(x_nr,y_nr,p) = Y_sd(x_nr,y_nr, min_index(x_nr,y_nr)); % Y_cd is the corresponding standard deviation between the relative flip angle values
end
end
spm_progress_bar('Set',p);
end
%-Save everything in OUTPUT dir
%-----------------------------------------------------------------------
% define generic output header
input_files = b1map_params.b1input;
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.procstep.descrip = 'B1+ map calculation (EPI SE/STE protocol)';
% save B1 map (still distorted and not smoothed)
Output_hdr.history.output.imtype = 'Distorted B1+ map';
Output_hdr.history.output.units = 'p.u.';
V_save = struct('fname',V(1).fname,'dim',V(1).dim,'mat',V(1).mat,'dt',V(1).dt,'descrip','B1 map [%]');
[~,outname,e] = fileparts(V_save.fname);
V_save.fname = fullfile(outpath,['B1map_' outname e]);
V_save = spm_write_vol(V_save,Y_ab*100);
set_metadata(V_save.fname,Output_hdr,json);
% save SD map (still distorted and not smoothed)
Output_hdr.history.output.imtype = 'Distorted SD (error) map';
Output_hdr.history.output.units = 'p.u.';
W_save = struct('fname',V(1).fname,'dim',V(1).dim,'mat',V(1).mat,'dt',V(1).dt,'descrip','SD [%]');
W_save.fname = fullfile(outpath,['SDmap_' outname e]);
W_save = spm_write_vol(W_save,Y_cd*100);
set_metadata(W_save.fname,Output_hdr,json);
% save SD map (still distorted and not smoothed)
Output_hdr.history.output.imtype = 'SSQ image';
Output_hdr.history.output.units = 'a.u.';
X_save = struct('fname',V(1).fname,'dim',V(1).dim,'mat',V(1).mat,'dt',V(1).dt,'descrip','SE SSQ matrix');
X_save.fname = fullfile(outpath,['SumOfSq' outname e]);
X_save = spm_write_vol(X_save,Ssq_matrix); %#ok<*NASGU>
set_metadata(X_save.fname,Output_hdr,json);
%-B0 undistortion
%-----------------------------------------------------------------------
% since B0 data will be coregistered and resliced with the B1 data, we copy
% them into the calcpath directory to avoid altering the the raw data:
Qtmp = cell(size(Q,1),1);
for i=1:size(Q,1)
Qtmp{i} = fullfile(outpath, spm_file(Q(i,:), 'filename'));
copyfile(Q(i,:), Qtmp{i});
try copyfile([spm_str_manip(Q(i,:),'r') '.json'],[spm_str_manip(Qtmp{i},'r') '.json']); end %#ok<*TRYNC>
end
Q = char(Qtmp);
% magnitude image
% NOTE: must strip the ',1' (at the end of the file extension '.nii,1')!!
magfnam = spm_file(Q(1,:),'number','');
% phase image
phasefnam = spm_file(Q(3,:),'number','');
% both fieldmap images
fmfnam = char(phasefnam,magfnam);
% image to be corrected ("anatomical" reference = SSQ image)
anatfnam = X_save.fname;
% other images to be corrected (distorted B1 and SD maps)
otherfnam{1} = V_save.fname;
otherfnam{2} = W_save.fname;
% unwarp
[fmap_img,unwarp_img] = hmri_create_B1Map_unwarp(fmfnam, anatfnam, otherfnam, b1map_params);
uanat_img{1} = unwarp_img{1}.fname;
ub1_img{1} = unwarp_img{2}.fname;
ustd_img{1} = unwarp_img{3}.fname;
% set metadata for unwrapped output images
% define generic header for B0-unwarp process
scphasefnam = fullfile(b1map_params.outpath, spm_file(spm_file(fmfnam(2,:),'prefix','sc'),'filename'));
input_files = cat(1,{anatfnam},{fmfnam(1,:)},{fmfnam(2,:)},otherfnam{1},otherfnam{2});
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.procstep.descrip = 'Unwarp B1 map (EPI SE/STE protocol)';
% set metadata for unwarped B1 image
Output_hdr.history.output.imtype = 'Unwarped B1 map';
Output_hdr.history.output.units = 'p.u.';
set_metadata(ub1_img{1},Output_hdr,json);
% set metadata for unwarped SD map
Output_hdr.history.output.imtype = 'Unwarped SD (error) map';
Output_hdr.history.output.units = 'p.u.';
set_metadata(ustd_img{1},Output_hdr,json);
% set metadata for unwarped SSQ map
Output_hdr.history.output.imtype = 'Unwarped SSQ image for anatomical reference';
Output_hdr.history.output.units = 'a.u.';
set_metadata(uanat_img{1},Output_hdr,json);
% set metadata for phase-unwrapped regularised field map (Hz) (fpm_* file)
Output_hdr.history.output.imtype = 'Phase-unwrapped regularised field map';
Output_hdr.history.output.units = 'Hz';
set_metadata(fmap_img{1}.fname,Output_hdr,json);
% set metadata for Voxel Displacement Map (vdm5_* file)
Output_hdr.history.output.imtype = 'Voxel displacement map';
Output_hdr.history.output.units = 'Vx';
set_metadata(fmap_img{2}.fname,Output_hdr,json);
% set metadata for phase map scaled between +/-pi (sc* file)
Output_hdr.history.output.imtype = 'Phase map rescaled between [-pi, pi]';
Output_hdr.history.output.units = 'Radians';
set_metadata(scphasefnam,Output_hdr,json);
%-B1 map processing (masking, padding, smoothing, ...)
%--------------------------------------------------------------------------
fpm_img{1} = fmap_img{1};
vdm_img{1} = fmap_img{2};
[allub1_img] = hmri_create_B1Map_process(ub1_img,ustd_img,vdm_img,fpm_img,b1map_params);
% set metadata for processing B1 images
% define generic header for B1 process
input_files = cat(1,ub1_img,ustd_img,vdm_img{1}.fname,fpm_img{1}.fname);
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.procstep.descrip = 'Process B1 map (EPI SE/STE protocol)';
% set metadata for each output
for i=1:length(allub1_img)
Output_hdr.history.output.imtype = allub1_img{i}.descrip;
Output_hdr.history.output.units = 'p.u.';
set_metadata(allub1_img{i}.fname,Output_hdr,json);
end
% set correct output for the current subfunction (unwrapped "anatomical"
% image (SSQ) for coregistration and final B1 map). For coherence among B1
% protocol, rename these files *_B1ref (for anatomical reference) and
% *_B1map (for B1+ bias map in p.u.):
B1map = fullfile(outpath,[outname '_B1map.nii']);
copyfile(allub1_img{2}.fname, B1map);
copyfile([spm_str_manip(allub1_img{2}.fname,'r') '.json'],[spm_str_manip(B1map,'r') '.json']);
B1ref = fullfile(outpath,[outname '_B1ref.nii']);
copyfile(uanat_img{1}, B1ref);
copyfile([spm_str_manip(uanat_img{1},'r') '.json'],[spm_str_manip(B1ref,'r') '.json']);
P_trans = char(B1ref, B1map);
end
%% =======================================================================%
% B1 map calculation - SIEMENS tfl_b1map protocol
% Written by Tobias Leutritz (based on calc_AFI_b1map by TL)
%=========================================================================%
function P_trans = calc_tfl_b1map(jobsubj, b1map_params)
json = hmri_get_defaults('json');
P = b1map_params.b1input(2,:); % scaled FA map from tfl_b1map sequence
Q = b1map_params.b1input(1,:); % anatomical image from tfl_b1map sequence
% read header information and volumes
V1 = spm_vol(P); % image volume information
V2 = spm_vol(Q);
Vol1 = spm_read_vols(V1);
Vol2 = spm_read_vols(V2);
alphanom = get_metadata_val(P,'FlipAngle'); % nominal flip angle of tfl_b1map
% generating the map
B1map_norm = abs(Vol1)*10/alphanom;
% smoothed map
smB1map_norm = zeros(size(B1map_norm));
pxs = sqrt(sum(V1.mat(1:3,1:3).^2)); % Voxel resolution
smth = 8./pxs;
spm_smooth(B1map_norm,smB1map_norm,smth);
% Save everything in OUTPUT dir
%-----------------------------------------------------------------------
% determine output directory path
outpath = jobsubj.path.b1path;
b1map_params.outpath = outpath;
sname = spm_file(V1.fname,'basename');
VB1 = V1;
VB1.pinfo = [max(smB1map_norm(:))/16384;0;0]; % what is this for? (TL)
VB1.fname = fullfile(outpath, [sname '_B1map.nii']);
VB1.descrip = 'Smoothed & normalised (p.u.) B1 bias map - TFL B1map protocol';
spm_write_vol(VB1,smB1map_norm);
% set and write metadata
input_files = cat(1,{V2.fname},{V1.fname});
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.procstep.descrip = 'B1+ map calculation (SIEMENS tfl_b1map protocol)';
set_metadata(VB1.fname,Output_hdr,json);
% copy also anatomical image to outpath to prevent modification of original data
anat_fname = fullfile(outpath, [spm_file(V2.fname, 'basename') '_B1ref.nii']);
copyfile(V2.fname, anat_fname);
try copyfile([spm_str_manip(V2.fname,'r') '.json'],[spm_str_manip(anat_fname,'r') '.json']); end %#ok<*TRYNC>
% requires anatomic image + map
P_trans = char(char(anat_fname),char(VB1.fname));
end
%% =======================================================================%
% B1 map calculation - SIEMENS rf_map protocol
% Written by Tobias Leutritz
%=========================================================================%
function P_trans = calc_rf_map(jobsubj, b1map_params)
json = hmri_get_defaults('json');
P = b1map_params.b1input(2,:); % scaled FA map from rf_map sequence
Q = b1map_params.b1input(1,:); % anatomical image from rf_map sequence
% read header information and volumes
V1 = spm_vol(P); % image volume information
V2 = spm_vol(Q);
Vol1 = spm_read_vols(V1);
Vol2 = spm_read_vols(V2);
% generating the map
B1map_norm = (abs(Vol1)-2048)*180*100/(90*2048); % *100/90 to get p.u.
% the formula (abs(Vol1)-2048)*180/2048 would result in an absolute FA map
% smoothed map
smB1map_norm = zeros(size(B1map_norm));
pxs = sqrt(sum(V1.mat(1:3,1:3).^2)); % Voxel resolution
smth = 8./pxs;
spm_smooth(B1map_norm,smB1map_norm,smth);
% Save everything in OUTPUT dir
%-----------------------------------------------------------------------
% determine output directory path
outpath = jobsubj.path.b1path;
b1map_params.outpath = outpath;
sname = spm_file(V1.fname,'basename');
VB1 = V1;
VB1.pinfo = [max(smB1map_norm(:))/16384;0;0]; % what is this for? (TL)
VB1.fname = fullfile(outpath, [sname '_B1map.nii']);
VB1.descrip = 'Smoothed & normalised (p.u.) B1 bias map - TFL B1map protocol';
spm_write_vol(VB1,smB1map_norm);
% set and write metadata
input_files = cat(1,{V2.fname},{V1.fname});
Output_hdr = init_b1_output_metadata(input_files, b1map_params);
Output_hdr.history.procstep.descrip = 'B1+ map calculation (SIEMENS rf_map protocol)';
set_metadata(VB1.fname,Output_hdr,json);
% copy also anatomical image to outpath to prevent modification of original data
anat_fname = fullfile(outpath, [spm_file(V2.fname, 'basename') '_B1ref.nii']);
copyfile(V2.fname, anat_fname);
try copyfile([spm_str_manip(V2.fname,'r') '.json'],[spm_str_manip(anat_fname,'r') '.json']); end %#ok<*TRYNC>
% requires anatomic image + map
P_trans = char(char(anat_fname),char(VB1.fname));
end
%% =======================================================================%
% Determine whether b1 data are available and whether any processing should
% be applied. If so, all the required parameters for b1map calculation are
% retrieved, including b1map and b0map acquisition parameters and
% processing parameters, if applicable. Check whether input data are
% coherent with the processing type selected. Missing parameters will be
% retrieved from the hmri_get_defaults.
%=========================================================================%
function b1map_params = get_b1map_params(jobsubj)
% retrieve b1 protocol from job
% (can be different - a variation of - the b1 type)
f = fieldnames(jobsubj.b1_type);
b1_protocol = f{1};
% load customized defaults parameters from customized defaults file if any
% (the customized defaults file must be run to overwrite the standard
% defaults parameters)
if isfield(jobsubj.b1_type.(b1_protocol),'b1parameters')
% first reinitialise processing parameters to standard defaults:
hmri_b1_standard_defaults;
% then, if customized defaults file available, run it to overwrite
% standard defaults parameters.
if isfield(jobsubj.b1_type.(b1_protocol).b1parameters,'b1defaults')
deffnam = jobsubj.b1_type.(b1_protocol).b1parameters.b1defaults;
spm('Run',deffnam);
end
end
% load all B1 bias correction defaults parameters
b1map_params = hmri_get_defaults(['b1map.' b1_protocol]);
fprintf(1,'\n\n---------------- B1 MAP CALCULATION (%s) ----------------\n',b1_protocol);
% load B1 input images if any
% (NB: if a 'b1input' field is present, it should NOT be empty)
if isfield(jobsubj.b1_type.(b1_protocol),'b1input')
b1map_params.b1input = char(spm_file(jobsubj.b1_type.(b1_protocol).b1input,'number',''));
if isempty(b1map_params.b1input)
fprintf(1,['\nWARNING: expected B1 input images missing. Switching to "no \n' ...
'\tB1 correction" mode. If you meant to apply B1 bias correction, \n' ...
'\tcheck your data and re-run the batch.\n']);
b1_protocol = 'no_B1_correction';
b1map_params = hmri_get_defaults('b1map.no_B1_correction');
end
end
% load B0 input images if any
% (NB: if a 'b0input' field is present, it may be empty)
if isfield(jobsubj.b1_type.(b1_protocol),'b0input')
b1map_params.b0input = char(spm_file(jobsubj.b1_type.(b1_protocol).b0input,'number',''));
if isempty(b1map_params.b0input)
% fprintf(1,['\nWARNING: expected B0 fieldmap not available for EPI undistortion.\n' ...
% '\tNo fieldmap correction will be applied.\n']);
% b1map_params.b0avail = false;
fprintf(1,['\nWARNING: expected B0 fieldmap not available for EPI undistortion.\n' ...
'\tThe current implementation does not allow you to apply EPI-based B1 bias \n' ...
'\tcorrection without phase unwrapping. Switching to "no B1 correction" mode.\n' ...
'\tIf you meant to apply B1 bias correction, check your data and re-run the batch.\n']);
b1_protocol = 'no_B1_correction';
b1map_params = hmri_get_defaults('b1map.no_B1_correction');
end
end
% process job inputs according to B1 type
switch b1_protocol
case 'UNICORT'
fprintf(1,'\nNo B1 map available. UNICORT will be applied.\n');
case 'no_B1_correction'
fprintf(1,'\nNo B1 map available. No B1 correction applied (semi-quantitative maps only)\n');
case 'pre_processed_B1'
if ~isempty(b1map_params.b1input)
fprintf(1,'\nPreprocessed B1 map available. Assuming it is in percent units. No calculation required.\n');
end
case 'i3D_EPI'
if ~isempty(b1map_params.b1input)
fprintf(1, '\nSE/STE EPI protocol selected ...\n');
b1hdr = get_metadata(b1map_params.b1input(1,:));
try
tmp = get_metadata_val(b1hdr{1},'B1mapNominalFAValues');
if isempty(tmp); fprintf(1,'\nWARNING: using defaults value instead of metadata');
else b1map_params.b1acq.beta = tmp; end
tmp = get_metadata_val(b1hdr{1},'B1mapMixingTime');
if isempty(tmp); fprintf(1,'\nWARNING: using defaults value instead of metadata');
else b1map_params.b1acq.TM = tmp; end
tmp = get_metadata_val(b1hdr{1},'epiReadoutDuration'); % must take into account PAT but not PF acceleration
if isempty(tmp); fprintf(1,'\nWARNING: using defaults value instead of metadata');
else b1map_params.b1acq.tert = tmp; end
tmp = get_metadata_val(b1hdr{1},'PhaseEncodingDirectionSign');
if isempty(tmp); fprintf(1,'\nWARNING: using defaults value instead of metadata');
else b1map_params.b1acq.blipDIR = tmp; end
if ~isempty(b1map_params.b0input)
% note that the current implementation assumes that
% b0 input images = 2 magnitude images (1st and 2nd
% echoes) and 1 presubtracted phase image.
tmp = get_metadata_val(b1map_params.b0input(1,:),'EchoTime');
if isempty(tmp); fprintf(1,'\nWARNING: using defaults value instead of metadata');
else b1map_params.b0acq.shortTE = tmp; end
tmp = get_metadata_val(b1map_params.b0input(2,:),'EchoTime');
if isempty(tmp); fprintf(1,'\nWARNING: using defaults value instead of metadata');
else b1map_params.b0acq.longTE = tmp; end
b1map_params.b0acq.iformat = 'PM';
end
catch %#ok<*CTCH>
fprintf(1, ['\nWARNING: possibly no metadata associated to the input images. \n' ...
'Default acquisition and processing parameters will be used.\n']);
end
end
case 'i3D_AFI'
if ~isempty(b1map_params.b1input)
fprintf(1, '\nAFI protocol selected ...\n');
b1hdr = get_metadata(b1map_params.b1input(1,:));
try
tr = get_metadata_val(b1hdr{1},'RepetitionTimes');
if isempty(tr); fprintf(1,'\nWARNING: using defaults value instead of metadata');
else b1map_params.b1acq.TR2TR1ratio = tr(2)/tr(1); end
tmp = get_metadata_val(b1hdr{1},'FlipAngle');
if isempty(tmp); fprintf(1,'\nWARNING: using defaults value instead of metadata');
else b1map_params.b1acq.alphanom = tmp; end
catch
fprintf(1, ['\nWARNING: possibly no metadata associated to the input images. \n' ...
'Default acquisition and processing parameters will be used.\n']);
end
end
case 'tfl_b1_map'
if ~isempty(b1map_params.b1input)
fprintf(1, '\nSIEMENS tfl_b1map protocol selected ...\n');
end
case 'rf_map'
if ~isempty(b1map_params.b1input)
fprintf(1, '\nSIEMENS rf_map protocol selected ...\n');
end
otherwise
fprintf(1, ['\nWARNING: something must have gone wrong in the JOB configuration.\n' ...
'\tUnknown B1 processing methods, assuming "no B1 correction" mode.\n']);
b1_protocol = 'no_B1_correction';
b1map_params = hmri_get_defaults('b1map.no_B1_correction');
end
% print acquisition and processing parameters
fprintf(1,'\n');
if isfield(b1map_params, 'b1acq')
fprintf(1,'B1 acquisition parameters:\n');
disp(b1map_params.b1acq);
end
if isfield(b1map_params, 'b0acq')
fprintf(1,'B0 acquisition parameters:\n');
disp(b1map_params.b0acq);
end
if isfield(b1map_params, 'b1proc')
fprintf(1,'B1 processing parameters:\n');
disp(b1map_params.b1proc);
end
fprintf(1, '\n');
end
%=========================================================================%
% To arrange the metadata structure for B1 map calculation output.
%=========================================================================%
function metastruc = init_b1_output_metadata(input_files, b1map_params)
proc.descrip = 'B1+ map calculation';
proc.version = hmri_get_version;
proc.params = b1map_params;
output.imtype = 'B1+ map';
output.units = 'p.u.';
metastruc = init_output_metadata_structure(input_files, proc, output);
end