-
Notifications
You must be signed in to change notification settings - Fork 11
/
Copy pathPsPM_References.lyx
13878 lines (10581 loc) · 234 KB
/
PsPM_References.lyx
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
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
#LyX 2.3 created this file. For more info see http://www.lyx.org/
\lyxformat 544
\begin_document
\begin_header
\save_transient_properties true
\origin unavailable
\textclass article
\begin_preamble
\definecolor{colKeys}{rgb}{0,0,1}
\definecolor{colIdentifier}{rgb}{0,0,0}
\definecolor{colComments}{rgb}{0.53, 0.66, 0.42}
\definecolor{colString}{rgb}{0.87, 0.36, 0.51}
\definecolor{barColor}{rgb}{0.43, 0.5, 0.5}
\renewcommand{\textendash}{--}
\renewcommand{\textemdash}{---}
\usepackage{bera}
\renewcommand*\l@subsection{\@dottedtocline{2}{1.8em}{3.2 em}}
\usepackage{enumitem}
\setlist[itemize]{noitemsep}
\end_preamble
\use_default_options true
\maintain_unincluded_children false
\language english
\language_package default
\inputencoding utf8
\fontencoding global
\font_roman "default" "default"
\font_sans "default" "default"
\font_typewriter "default" "default"
\font_math "auto" "auto"
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100 100
\font_tt_scale 100 100
\use_microtype false
\use_dash_ligatures true
\graphics default
\default_output_format default
\output_sync 0
\bibtex_command default
\index_command default
\paperfontsize 10
\spacing single
\use_hyperref false
\papersize default
\use_geometry true
\use_package amsmath 1
\use_package amssymb 1
\use_package cancel 1
\use_package esint 1
\use_package mathdots 1
\use_package mathtools 1
\use_package mhchem 1
\use_package stackrel 1
\use_package stmaryrd 1
\use_package undertilde 1
\cite_engine basic
\cite_engine_type default
\biblio_style plain
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
\justification true
\use_refstyle 1
\use_minted 0
\index Index
\shortcut idx
\color #008000
\end_index
\leftmargin 1in
\secnumdepth 3
\tocdepth 3
\paragraph_separation indent
\paragraph_indentation default
\is_math_indent 0
\math_numbering_side default
\quotes_style english
\dynamic_quotes 0
\papercolumns 1
\papersides 1
\paperpagestyle default
\listings_params "language=Matlab,float=hbp,basicstyle={\footnotesize\ttfamily},identifierstyle={\color{colIdentifier}},keywordstyle={\color{colKeys}},stringstyle={\color{colString}},commentstyle={\itshape\color{colComments}},columns=fixed,tabsize=2,extendedchars=true,showspaces=false,showstringspaces=false,captionpos=t,backgroundcolor={\color{white}},framexleftmargin=1pt,frame=l"
\tracking_changes false
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
\end_header
\begin_body
\begin_layout Title
PsPM: Option References
\end_layout
\begin_layout Standard
\align center
Version 6.1.2
\end_layout
\begin_layout Standard
\begin_inset VSpace defskip
\end_inset
\end_layout
\begin_layout Standard
\align center
by the PsPM team
\begin_inset Foot
status open
\begin_layout Plain Layout
\noindent
If you have comments on or error corrections to this documentation, please
send them to the PsPM team or post them on:
\begin_inset CommandInset href
LatexCommand href
name "bachlab.org/pspm"
target "http://bachlab.org/pspm"
literal "false"
\end_inset
\end_layout
\end_inset
\size larger
:
\end_layout
\begin_layout Standard
\align center
Dominik R Bach, Giuseppe Castegnetti, Laure Ciernik, Samuel Gerster, Saurabh
Khemka, Christoph Korn, Samuel Maxwell, Tobias Moser, Philipp C Paulus,
Ivan Rojkov, Matthias Staib, Eshref Yozdemir, Teddy Zhao and collaborators
\end_layout
\begin_layout Standard
\align center
\begin_inset Newpage newpage
\end_inset
\end_layout
\begin_layout Standard
\begin_inset CommandInset toc
LatexCommand tableofcontents
\end_inset
\begin_inset Newpage newpage
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Newpage pagebreak
\end_inset
\end_layout
\begin_layout Section
Introduction
\end_layout
\begin_layout Standard
Since version 6.1, PsPM has started using
\family typewriter
pspm_options
\family default
to control field values in most functions.
The default values for option fields have been set in
\family typewriter
pspm_options
\family default
and described in this document with their explanations wherever available.
The values of option fields have their own specification requirements and
should be set carefully if non-standard values are used.
Please check this document carefully about how to set values for the option
fields.
The errors which may appear when such variables have been set according
to this guideline should be sent to PsPM developer team for getting further
support.
\end_layout
\begin_layout Section
Index
\end_layout
\begin_layout Subsection
Field name
\end_layout
\begin_layout Itemize
A word written in bold means the name of a variable.
\end_layout
\begin_deeper
\begin_layout Itemize
Example:
\series bold
channel
\end_layout
\end_deeper
\begin_layout Subsection
Data type
\end_layout
\begin_layout Standard
There are five basic kinds of data types used for the values of the fields
in PsPM, which are namely
\shape italic
cell
\shape default
,
\shape italic
character
\shape default
(abbreviated as
\shape italic
char
\shape default
),
\shape italic
double
\shape default
,
\shape italic
logical
\shape default
, and
\shape italic
struct
\shape default
.
Among
\shape italic
double
\shape default
, there are some values required to be
\shape italic
integers
\shape default
for their actual meanings.
There are also some values required to be more than
\begin_inset Formula $1\times1$
\end_inset
size, and there are therefore denoted as
\shape italic
double (vector)
\shape default
or
\shape italic
double (matrix)
\shape default
.
If unspecified,
\shape italic
double (vector)
\shape default
denotes a matrix of size
\begin_inset Formula $1\times n$
\end_inset
.
If such vectors / matrixes are additionally required to be
\shape italic
integers
\shape default
, they will be specified as
\shape italic
integer (vector)
\shape default
or
\shape italic
integer (matrix)
\shape default
.
\end_layout
\begin_layout Subsection
Unit
\end_layout
\begin_layout Standard
Content in this column demonstrates the unit of default and acceptable values
of this field.
This column will not be available for the tables when there are no variables
with physical meaning and units.
\end_layout
\begin_layout Subsection
Default value
\end_layout
\begin_layout Standard
Default values are used if users have not customised the fields.
\end_layout
\begin_layout Itemize
A word written in typewritter format means a string that is used in the
code, typically the value of a variable.
\end_layout
\begin_deeper
\begin_layout Itemize
Example:
\family typewriter
add
\end_layout
\end_deeper
\begin_layout Itemize
A number written in typewritter denotes a number used in the code, typically
the value of a variable.
\end_layout
\begin_deeper
\begin_layout Itemize
Example:
\family typewriter
1
\end_layout
\end_deeper
\begin_layout Subsection
Acceptable values
\end_layout
\begin_layout Standard
Apart from the notations described above for the default values, two additional
terms, Any and Subset, are also used:
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
Any
\family default
\shape italic
Any
\shape default
means any value that meets the requirement of data type can be used here.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
Subset
\family default
\shape italic
Subset
\shape default
means any value that is a subset of the default value can be used here.
\end_layout
\begin_layout Section
References for Values
\end_layout
\begin_layout Subsection
Abbreviations
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
amri
\family default
Advanced Magnetic Resonance Imaging
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
au
\family default
Arbitrary Unit
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
dcm
\family default
Dynamic Causal Modelling
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
ecg
\family default
Electrocardiogram
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
emg
\family default
Electromyography
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
hb
\family default
Heart Beat
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
hp
\family default
Heart Period
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
tam
\family default
Trial Average Model
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
pp
\family default
PreProcessing
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
resp
\family default
Respiration
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
rf
\family default
Response Function
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
scr
\family default
Skin Conductance Response
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
sf
\family default
Spontaneous Fluctuations
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
sps
\family default
ScanPath Speed
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
teo
\family default
Teager Energy Operator
\end_layout
\begin_layout Subsection
Action Descriptors
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
channel_action
\end_layout
\begin_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
none
\family default
No channel action will be performed.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
add
\family default
The results will be added as a new channel.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
replace
\family default
The results will replace the old data in the corresponding channel.
If no corresponding channel is available, the results will be added as
a new channel.
\end_layout
\end_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
channel_output
\end_layout
\begin_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
all
\family default
All markers are to be added.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
corrected
\family default
Only markers which have been assigned are to be added.
\end_layout
\end_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
eyes
\end_layout
\begin_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
combined
\family default
Combined bilateral eyes that are computed based on the left and right eyes.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
left
\family default
Left eye.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
right
\family default
Right eye.
\end_layout
\end_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
nan_output
\end_layout
\begin_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
none
\family default
Values not to be displayed on the screen or written into files.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
screen
\family default
Values to be displayed on MATLAB's screen.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
file_output
\family default
Values to be written into a created file.
\end_layout
\end_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
statstype
\end_layout
\begin_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
param
\family default
Export all parameter estimates.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
cond
\family default
Contrasts formulated in terms of conditions.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
recon
\family default
Export all conditions.
\end_layout
\end_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
timeunit
\end_layout
\begin_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
seconds
\family default
\shape italic
Second
\shape default
as the unit.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
samples
\family default
\shape italic
Sample
\shape default
as the unit.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
markers
\family default
\shape italic
Marker
\shape default
as the unit.
\end_layout
\end_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
overwrite
\end_layout
\begin_deeper
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
1
\family default
The results will be overwrite.
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
0
\family default
The results will be dropped out.
\end_layout
\end_deeper
\begin_layout Subsection
Miscellaneous
\end_layout
\begin_layout Labeling
\labelwidthstring 00.00.0000
\family typewriter
NS
\family default
The parameter does not have a default value.
\end_layout
\begin_layout Section
Function-specific Default Values
\end_layout
\begin_layout Subsection
Blink Saccade Filter
\end_layout
\begin_layout Standard
\noindent
\align center
\series bold
Table 1
\series default
Default values for
\family typewriter
pspm_blink_saccade_filt
\end_layout
\begin_layout Standard
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="4">
<features booktabs="true" tabularvalignment="middle" tabularwidth="100line%">
<column alignment="left" valignment="top" width="0pt">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<row>
<cell alignment="left" valignment="top" topline="true" bottomline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\series bold
Field name
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\series bold
Data type
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\series bold
Default value
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\series bold
Acceptable values
\end_layout
\end_inset
</cell>
</row>
<row>
<cell alignment="left" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\family typewriter
\series bold
channel
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
cell / char / integer
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\family typewriter
0
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
Any
\end_layout
\end_inset
</cell>
</row>
<row>
<cell alignment="left" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\family typewriter
\series bold
channel_action
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
char
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\family typewriter
add
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\family typewriter
replace
\end_layout
\end_inset
</cell>
</row>
</lyxtabular>
\end_inset
\end_layout
\begin_layout Subsection
Contrasts on the 1st Level
\end_layout
\begin_layout Standard
\noindent
\align center
\series bold
Table 3
\series default
Default values for
\family typewriter
pspm_con1
\end_layout
\begin_layout Standard
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="4">
<features booktabs="true" tabularvalignment="middle" tabularwidth="100line%">
<column alignment="left" valignment="top" width="0pt">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<row>
<cell alignment="left" valignment="top" topline="true" bottomline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\series bold
Field name
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\series bold
Data type
\end_layout
\end_inset
</cell>