ENH: Support TD data

.mailmap

@@ -352,5 +352,6 @@ Yousra Bekhti <[email protected]> Yoursa BEKHTI <[email protected]
 Yousra Bekhti <[email protected]> Yoursa BEKHTI <[email protected]>
 Yousra Bekhti <[email protected]> Yousra BEKHTI <[email protected]>
 Yousra Bekhti <[email protected]> yousrabk <[email protected]>
+Zahra M. Aghajan <[email protected]> Zahra M. Aghajan <[email protected]>
 Zhi Zhang <[email protected]> ZHANG Zhi <[email protected]>
 Zhi Zhang <[email protected]> ZHANG Zhi <[email protected]>

doc/changes/devel/11064.newfeature.rst

@@ -0,0 +1 @@
+Added basic support for TD fNIRS data, by :newcontrib:`Zahra Aghajan`, :newcontrib:`Julien Dubois`, :newcontrib:`John Griffiths`, `Robert Luke`_, and `Eric Larson`_.

doc/changes/names.inc

@@ -137,6 +137,7 @@
 .. _Joan Massich: https://github.com/massich
 .. _Johann Benerradi: https://github.com/HanBnrd
 .. _Johannes Niediek: https://github.com/jniediek
+.. _John Griffiths: https://www.grifflab.com
 .. _John Samuelsson: https://github.com/johnsam7
 .. _John Veillette: https://psychology.uchicago.edu/directory/john-veillette
 .. _Jon Houck: https://www.mrn.org/people/jon-m.-houck/principal-investigators
@@ -150,6 +151,7 @@
 .. _Judy D Zhu: https://github.com/JD-Zhu
 .. _Juergen Dammers: https://github.com/jdammers
 .. _Jukka Nenonen: https://www.linkedin.com/pub/jukka-nenonen/28/b5a/684
+.. _Julien Dubois: https://github.com/julien-dubois-k
 .. _Jussi Nurminen: https://github.com/jjnurminen
 .. _Kaisu Lankinen: http://bishoplab.berkeley.edu/Kaisu.html
 .. _Katarina Slama: https://github.com/katarinaslama
@@ -314,5 +316,6 @@
 .. _Yiping Zuo: https://github.com/frostime
 .. _Yousra Bekhti: https://www.linkedin.com/pub/yousra-bekhti/56/886/421
 .. _Yu-Han Luo: https://github.com/yh-luo
+.. _Zahra Aghajan: https://github.com/Zahra-M-Aghajan
 .. _Zhi Zhang: https://github.com/tczhangzhi/
 .. _Zvi Baratz: https://github.com/ZviBaratz

mne/_fiff/pick.py

@@ -104,6 +104,16 @@ def get_channel_type_constants(include_defaults=False):
             unit=FIFF.FIFF_UNIT_RAD,
             coil_type=FIFF.FIFFV_COIL_FNIRS_FD_PHASE,
         ),
+        fnirs_td_gated_amplitude=dict(
+            kind=FIFF.FIFFV_FNIRS_CH,
+            unit=FIFF.FIFF_UNIT_V,
+            coil_type=FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE,
+        ),
+        fnirs_td_moments_amplitude=dict(
+            kind=FIFF.FIFFV_FNIRS_CH,
+            unit=FIFF.FIFF_UNIT_V,
+            coil_type=FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE,
+        ),
         fnirs_od=dict(kind=FIFF.FIFFV_FNIRS_CH, coil_type=FIFF.FIFFV_COIL_FNIRS_OD),
         hbo=dict(
             kind=FIFF.FIFFV_FNIRS_CH,
@@ -197,6 +207,8 @@ def get_channel_type_constants(include_defaults=False):
             FIFF.FIFFV_COIL_FNIRS_FD_AC_AMPLITUDE: "fnirs_fd_ac_amplitude",
             FIFF.FIFFV_COIL_FNIRS_FD_PHASE: "fnirs_fd_phase",
             FIFF.FIFFV_COIL_FNIRS_OD: "fnirs_od",
+            FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE: "fnirs_td_gated_amplitude",
+            FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE: "fnirs_td_moments_amplitude",
         },
     ),
     "eeg": (
@@ -385,6 +397,16 @@ def _triage_fnirs_pick(ch, fnirs, warned):
         return True
     elif ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_OD and "fnirs_od" in fnirs:
         return True
+    elif (
+        ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE
+        and "fnirs_td_moments_amplitude" in fnirs
+    ):
+        return True
+    elif (
+        ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE
+        and "fnirs_td_gated_amplitude" in fnirs
+    ):
+        return True
     return False
 
 
@@ -569,7 +591,7 @@ def pick_types(
                 pick[k] = _triage_meg_pick(info["chs"][k], ref_meg)
             elif ch_type in ("eyegaze", "pupil"):
                 pick[k] = _triage_eyetrack_pick(info["chs"][k], eyetrack)
-            else:  # ch_type in ('hbo', 'hbr')
+            else:  # ch_type in ('hbo', 'hbr', ...)
                 pick[k] = _triage_fnirs_pick(info["chs"][k], fnirs, warned)
 
     # restrict channels to selection if provided
@@ -862,6 +884,8 @@ def channel_indices_by_type(info, picks=None):
         fnirs_fd_ac_amplitude=list(),
         fnirs_fd_phase=list(),
         fnirs_od=list(),
+        fnirs_td_gated_amplitude=list(),
+        fnirs_td_moments_amplitude=list(),
         eyegaze=list(),
         pupil=list(),
     )
@@ -1099,6 +1123,8 @@ def _check_excludes_includes(chs, info=None, allow_bads=False):
     "fnirs_fd_ac_amplitude",
     "fnirs_fd_phase",
     "fnirs_od",
+    "fnirs_td_moments_amplitude",
+    "fnirs_td_gated_amplitude",
 )
 _EYETRACK_CH_TYPES_SPLIT = ("eyegaze", "pupil")
 _DATA_CH_TYPES_ORDER_DEFAULT = (

mne/cov.py

@@ -1521,6 +1521,7 @@ def __init__(
         grad=0.1,
         mag=0.1,
         eeg=0.1,
+        *,
         seeg=0.1,
         ecog=0.1,
         hbo=0.1,
@@ -1529,6 +1530,8 @@ def __init__(
         fnirs_fd_ac_amplitude=0.1,
         fnirs_fd_phase=0.1,
         fnirs_od=0.1,
+        fnirs_td_gated_amplitude=0.1,
+        fnirs_td_moments_amplitude=0.1,
         csd=0.1,
         dbs=0.1,
         store_precision=False,
@@ -1908,6 +1911,7 @@ def regularize(
     eeg=0.1,
     exclude="bads",
     proj=True,
+    *,
     seeg=0.1,
     ecog=0.1,
     hbo=0.1,
@@ -1916,6 +1920,8 @@ def regularize(
     fnirs_fd_ac_amplitude=0.1,
     fnirs_fd_phase=0.1,
     fnirs_od=0.1,
+    fnirs_td_gated_amplitude=0.1,
+    fnirs_td_moments_amplitude=0.1,
     csd=0.1,
     dbs=0.1,
     rank=None,
@@ -1967,6 +1973,10 @@ def regularize(
         Regularization factor for fNIRS raw phase signals.
     fnirs_od : float (default 0.1)
         Regularization factor for fNIRS optical density signals.
+    fnirs_td_gated_amplitude : float (default 0.1)
+        Regularization factor for fNIRS time domain gated amplitude signals.
+    fnirs_td_moments_amplitude : float (default 0.1)
+        Regularization factor for fNIRS time domain moments amplitude signals.
     csd : float (default 0.1)
         Regularization factor for EEG-CSD signals.
     dbs : float (default 0.1)
@@ -2007,6 +2017,8 @@ def regularize(
         fnirs_fd_ac_amplitude=fnirs_fd_ac_amplitude,
         fnirs_fd_phase=fnirs_fd_phase,
         fnirs_od=fnirs_od,
+        fnirs_td_gated_amplitude=fnirs_td_gated_amplitude,
+        fnirs_td_moments_amplitude=fnirs_td_moments_amplitude,
         csd=csd,
     )
 

mne/defaults.py

@@ -32,6 +32,8 @@
         fnirs_fd_ac_amplitude="k",
         fnirs_fd_phase="k",
         fnirs_od="k",
+        fnirs_td_gated_amplitude="k",
+        fnirs_td_moments_amplitude="k",
         csd="k",
         whitened="k",
         gsr="#666633",
@@ -60,6 +62,8 @@
         fnirs_fd_ac_amplitude="V",
         fnirs_fd_phase="rad",
         fnirs_od="V",
+        fnirs_td_gated_amplitude="M",
+        fnirs_td_moments_amplitude="M",
         csd="V/m²",
         whitened="Z",
         gsr="S",
@@ -88,6 +92,8 @@
         fnirs_fd_ac_amplitude="V",
         fnirs_fd_phase="rad",
         fnirs_od="V",
+        fnirs_td_gated_amplitude="µM",
+        fnirs_td_moments_amplitude="µM",
         csd="mV/m²",
         whitened="Z",
         gsr="S",
@@ -117,6 +123,8 @@
         fnirs_fd_ac_amplitude=1.0,
         fnirs_fd_phase=1.0,
         fnirs_od=1.0,
+        fnirs_td_gated_amplitude=1e6,
+        fnirs_td_moments_amplitude=1e6,
         csd=1e3,
         whitened=1.0,
         gsr=1.0,
@@ -151,6 +159,8 @@
         fnirs_fd_ac_amplitude=2e-2,
         fnirs_fd_phase=2e-1,
         fnirs_od=2e-2,
+        fnirs_td_gated_amplitude=1.0,
+        fnirs_td_moments_amplitude=1.0,
         csd=200e-4,
         dipole=1e-7,
         gof=1e2,
@@ -206,6 +216,8 @@
         fnirs_fd_phase="fNIRS (FD phase)",
         fnirs_od="fNIRS (OD)",
         hbr="Deoxyhemoglobin",
+        fnirs_td_gated_amplitude="fNIRS (TD amplitude)",
+        fnirs_td_moments_amplitude="fNIRS (TD moment)",
         gof="Goodness of fit",
         csd="Current source density",
         stim="Stimulus",