Feature/td nirs snirf

.github/workflows/tests.yml

@@ -150,6 +150,11 @@ jobs:
       - run: python ./tools/github_actions_check_old_env.py
         if: matrix.kind == 'old'
       # Minimal commands on Linux (macOS stalls)
+      - uses: actions/cache@v5
+        with:
+          key: minimal-commands-0
+          path: ~/minimal_cmds
+        if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old'
       - run: bash ./tools/get_minimal_commands.sh
         if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old'
       - run: bash ./tools/github_actions_infos.sh

.mailmap

@@ -379,6 +379,7 @@ Yousra Bekhti <yousra.bekhti@gmail.com> Yoursa BEKHTI <ybekhti@is222485.intra.ce
 Yousra Bekhti <yousra.bekhti@gmail.com> Yoursa BEKHTI <yousra.bekhti@gmail.com>
 Yousra Bekhti <yousra.bekhti@gmail.com> Yousra BEKHTI <yousra.bekhti@gmail.com>
 Yousra Bekhti <yousra.bekhti@gmail.com> yousrabk <yousra.bekhti@gmail.com>
+Zahra M. Aghajan <zahraa.aghajani@gmail.com> Zahra M. Aghajan <zahraa.aghajani@gmail.com>
 Zhi Zhang <850734033@qq.com> ZHANG Zhi <850734033@qq.com>
 Zhi Zhang <850734033@qq.com> ZHANG Zhi <zhi271.zhang@connect.polyu.hk>
 Ziyi ZENG <ziyizeng@link.cuhk.edu.cn> ZIYI ZENG <CME1909120@XMU.EDU.MY>

azure-pipelines.yml

@@ -89,6 +89,10 @@ stages:
               ./tools/setup_xvfb.sh
               sudo apt install -yq tcsh
             displayName: Install Ubuntu dependencies
+          - task: Cache@2
+            inputs:
+              key: minimal-cmds-0
+              path: /home/vsts/minimal_cmds
           - bash: ./tools/get_minimal_commands.sh
             displayName: Get minimal commands
           - bash: |

doc/changes/dev/13938.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

@@ -161,6 +161,7 @@
 .. _Johann Benerradi: https://github.com/HanBnrd
 .. _Johannes Herforth: https://herforth.net
 .. _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
@@ -174,6 +175,7 @@
 .. _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/jcrdubois
 .. _Jussi Nurminen: https://github.com/jjnurminen
 .. _Kaisu Lankinen: http://bishoplab.berkeley.edu/Kaisu.html
 .. _Kalle Makela: https://github.com/Kallemakela
@@ -376,6 +378,7 @@
 .. _Yixiao Shen: https://github.com/SYXiao2002
 .. _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/
 .. _Ziyi ZENG: https://github.com/ZiyiTsang
 .. _Zvi Baratz: https://github.com/ZviBaratz

doc/conf.py

@@ -190,6 +190,8 @@
         ),
     )
 )
+# Broken as of 2026/06/08 (https://github.com/joblib/joblib/issues/1796)
+intersphinx_mapping["joblib"] = ("https://joblib.readthedocs.io/en/stable", None)
 
 
 # NumPyDoc configuration -----------------------------------------------------

mne/_fiff/constants.py

@@ -931,6 +931,7 @@
 FIFF.FIFF_UNIT_LM = 115  # lumen
 FIFF.FIFF_UNIT_LX = 116  # lux
 FIFF.FIFF_UNIT_V_M2 = 117  # V/m^2
+FIFF.FIFF_UNIT_SEC2 = 118  # second^2
 #
 # Others we need
 #
@@ -972,6 +973,7 @@
         FIFF.FIFF_UNIT_LM,
         FIFF.FIFF_UNIT_LX,
         FIFF.FIFF_UNIT_V_M2,
+        FIFF.FIFF_UNIT_SEC2,
         FIFF.FIFF_UNIT_T_M,
         FIFF.FIFF_UNIT_AM,
         FIFF.FIFF_UNIT_AM_M2,
@@ -1044,7 +1046,9 @@
 FIFF.FIFFV_COIL_FNIRS_FD_PHASE = 305  # fNIRS frequency domain phase
 FIFF.FIFFV_COIL_FNIRS_RAW = FIFF.FIFFV_COIL_FNIRS_CW_AMPLITUDE  # old alias
 FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE = 306  # fNIRS time-domain gated amplitude
-FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE = 307  # fNIRS time-domain moments amplitude
+FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_INTENSITY = 307  # fNIRS time-domain moments intensity
+FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_MEAN = 308  # fNIRS time-domain moments mean
+FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_VARIANCE = 309  # fNIRS time-domain moments variance
 
 FIFF.FIFFV_COIL_EYETRACK_POS = 400  # Eye-tracking gaze position
 FIFF.FIFFV_COIL_EYETRACK_PUPIL = 401  # Eye-tracking pupil size
@@ -1145,7 +1149,9 @@
         FIFF.FIFFV_COIL_FNIRS_FD_AC_AMPLITUDE,
         FIFF.FIFFV_COIL_FNIRS_FD_PHASE,
         FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE,
-        FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE,
+        FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_INTENSITY,
+        FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_MEAN,
+        FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_VARIANCE,
         FIFF.FIFFV_COIL_MCG_42,
         FIFF.FIFFV_COIL_EYETRACK_POS,
         FIFF.FIFFV_COIL_EYETRACK_PUPIL,

mne/_fiff/meas_info.py

@@ -450,6 +450,7 @@ def set_montage(
     FIFF.FIFF_UNIT_NONE: "NA",
     FIFF.FIFF_UNIT_CEL: "C",
     FIFF.FIFF_UNIT_S: "S",
+    FIFF.FIFF_UNIT_SEC: "s",
     FIFF.FIFF_UNIT_PX: "px",
 }
 

mne/_fiff/pick.py

@@ -104,6 +104,26 @@ 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_UNITLESS,
+            coil_type=FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE,
+        ),
+        fnirs_td_moments_intensity=dict(
+            kind=FIFF.FIFFV_FNIRS_CH,
+            unit=FIFF.FIFF_UNIT_UNITLESS,
+            coil_type=FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_INTENSITY,
+        ),
+        fnirs_td_moments_mean=dict(
+            kind=FIFF.FIFFV_FNIRS_CH,
+            unit=FIFF.FIFF_UNIT_SEC,
+            coil_type=FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_MEAN,
+        ),
+        fnirs_td_moments_variance=dict(
+            kind=FIFF.FIFFV_FNIRS_CH,
+            unit=FIFF.FIFF_UNIT_SEC2,
+            coil_type=FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_VARIANCE,
+        ),
         fnirs_od=dict(kind=FIFF.FIFFV_FNIRS_CH, coil_type=FIFF.FIFFV_COIL_FNIRS_OD),
         hbo=dict(
             kind=FIFF.FIFFV_FNIRS_CH,
@@ -197,6 +217,10 @@ 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_INTENSITY: "fnirs_td_moments_intensity",
+            FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_MEAN: "fnirs_td_moments_mean",
+            FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_VARIANCE: "fnirs_td_moments_variance",
         },
     ),
     "eeg": (
@@ -385,6 +409,26 @@ 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_GATED_AMPLITUDE
+        and "fnirs_td_gated_amplitude" in fnirs
+    ):
+        return True
+    elif (
+        ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_INTENSITY
+        and "fnirs_td_moments_intensity" in fnirs
+    ):
+        return True
+    elif (
+        ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_MEAN
+        and "fnirs_td_moments_mean" in fnirs
+    ):
+        return True
+    elif (
+        ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_VARIANCE
+        and "fnirs_td_moments_variance" in fnirs
+    ):
+        return True
     return False
 
 
@@ -569,7 +613,7 @@ 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
@@ -867,6 +911,10 @@ def channel_indices_by_type(info, picks=None, *, exclude=()):
         fnirs_fd_ac_amplitude=list(),
         fnirs_fd_phase=list(),
         fnirs_od=list(),
+        fnirs_td_gated_amplitude=list(),
+        fnirs_td_moments_intensity=list(),
+        fnirs_td_moments_mean=list(),
+        fnirs_td_moments_variance=list(),
         eyegaze=list(),
         pupil=list(),
     )
@@ -1104,6 +1152,10 @@ def _check_excludes_includes(chs, info=None, allow_bads=False):
     "fnirs_fd_ac_amplitude",
     "fnirs_fd_phase",
     "fnirs_od",
+    "fnirs_td_gated_amplitude",
+    "fnirs_td_moments_intensity",
+    "fnirs_td_moments_mean",
+    "fnirs_td_moments_variance",
 )
 _EYETRACK_CH_TYPES_SPLIT = ("eyegaze", "pupil")
 _DATA_CH_TYPES_ORDER_DEFAULT = (

mne/_fiff/tests/test_constants.py

@@ -28,11 +28,14 @@
 
 # https://github.com/mne-tools/fiff-constants/commits/master
 REPO = "mne-tools"
-COMMIT = "e27f68cbf74dbfc5193ad429cc77900a59475181"
+COMMIT = "9ccb09d69daa8332f2e7252638ba397b60ba2502"
 
 # These are oddities that we won't address:
 iod_dups = (355, 359)  # these are in both MEGIN and MNE files
-tag_dups = (3501,)  # in both MEGIN and MNE files
+tag_dups = (  # in both MEGIN and MNE files
+    3501,  # FIFF.FIFF_XPLOTTER_LAYOUT
+    3507,  # FIFF.FIFF_MNE_CH_NAME_LIST
+)
 
 _dir_ignore_names = (
     "clear",
@@ -91,7 +94,9 @@
     304,  # fNIRS frequency domain AC amplitude
     305,  # fNIRS frequency domain phase
     306,  # fNIRS time domain gated amplitude
-    307,  # fNIRS time domain moments amplitude
+    307,  # fNIRS time domain moments intensity
+    308,  # fNIRS time domain moments mean
+    309,  # fNIRS time domain moments variance
     400,  # Eye-tracking gaze position
     401,  # Eye-tracking pupil size
     1000,  # For testing the MCG software

mne/cov.py

@@ -1538,6 +1538,7 @@ def __init__(
         grad=0.1,
         mag=0.1,
         eeg=0.1,
+        *,
         seeg=0.1,
         ecog=0.1,
         hbo=0.1,
@@ -1546,6 +1547,10 @@ 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_intensity=0.1,
+        fnirs_td_moments_mean=0.1,
+        fnirs_td_moments_variance=0.1,
         csd=0.1,
         dbs=0.1,
         store_precision=False,
@@ -1566,6 +1571,10 @@ def __init__(
         self.fnirs_fd_ac_amplitude = fnirs_fd_ac_amplitude
         self.fnirs_fd_phase = fnirs_fd_phase
         self.fnirs_od = fnirs_od
+        self.fnirs_td_gated_amplitude = fnirs_td_gated_amplitude
+        self.fnirs_td_moments_intensity = fnirs_td_moments_intensity
+        self.fnirs_td_moments_mean = fnirs_td_moments_mean
+        self.fnirs_td_moments_variance = fnirs_td_moments_variance
         self.csd = csd
         self.store_precision = store_precision
         self.assume_centered = assume_centered
@@ -1598,6 +1607,15 @@ def fit(self, X):
             dbs=self.dbs,
             hbo=self.hbo,
             hbr=self.hbr,
+            fnirs_cw_amplitude=self.fnirs_cw_amplitude,
+            fnirs_fd_ac_amplitude=self.fnirs_fd_ac_amplitude,
+            fnirs_fd_phase=self.fnirs_fd_phase,
+            fnirs_od=self.fnirs_od,
+            fnirs_td_gated_amplitude=self.fnirs_td_gated_amplitude,
+            fnirs_td_moments_intensity=self.fnirs_td_moments_intensity,
+            fnirs_td_moments_mean=self.fnirs_td_moments_mean,
+            fnirs_td_moments_variance=self.fnirs_td_moments_variance,
+            csd=self.csd,
             rank="full",
         )
         self.estimator_.covariance_ = self.covariance_ = cov_.data
@@ -1926,6 +1944,7 @@ def regularize(
     eeg=0.1,
     exclude="bads",
     proj=True,
+    *,
     seeg=0.1,
     ecog=0.1,
     hbo=0.1,
@@ -1934,6 +1953,10 @@ 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_intensity=0.1,
+    fnirs_td_moments_mean=0.1,
+    fnirs_td_moments_variance=0.1,
     csd=0.1,
     dbs=0.1,
     rank=None,
@@ -1985,6 +2008,14 @@ 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_intensity : float (default 0.1)
+        Regularization factor for fNIRS time domain moments amplitude signals.
+    fnirs_td_moments_mean : float (default 0.1)
+        Regularization factor for fNIRS time domain moments mean signals.
+    fnirs_td_moments_variance : float (default 0.1)
+        Regularization factor for fNIRS time domain moments variance signals.
     csd : float (default 0.1)
         Regularization factor for EEG-CSD signals.
     dbs : float (default 0.1)
@@ -2025,6 +2056,10 @@ 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_intensity=fnirs_td_moments_intensity,
+        fnirs_td_moments_mean=fnirs_td_moments_mean,
+        fnirs_td_moments_variance=fnirs_td_moments_variance,
         csd=csd,
     )