From fecef0b05a6d7390fa46283d46045941dd29c3fb Mon Sep 17 00:00:00 2001 From: Konstantinos Tsilimparis Date: Mon, 7 Apr 2025 17:26:04 +0200 Subject: [PATCH 01/12] ENH: add ctf275 montage This is based on the channel positions and orientations provided by fieldtrip: https://github.com/fieldtrip/fieldtrip/blob/master/template/gradiometer/ctf275.mat --- mne/channels/data/montages/ctf275.txt | 305 ++++++++++++++++++++++++++ 1 file changed, 305 insertions(+) create mode 100644 mne/channels/data/montages/ctf275.txt diff --git a/mne/channels/data/montages/ctf275.txt b/mne/channels/data/montages/ctf275.txt new file mode 100644 index 00000000000..d694ffc58ca --- /dev/null +++ b/mne/channels/data/montages/ctf275.txt @@ -0,0 +1,305 @@ +Name x y z ex ey ez +MLC11 0.086 0.0103 0.1355 0.346 0.0418 0.9373 +MLC12 0.0742 0.0286 0.1379 0.2638 0.1842 0.9468 +MLC13 0.0659 0.0488 0.1335 0.2456 0.3738 0.8944 +MLC14 0.0535 0.0678 0.1269 0.2278 0.5748 0.786 +MLC15 0.0403 0.0822 0.1182 0.1537 0.6329 0.7588 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-0.0261 0.0198 0.9452 -0.3265 0.0044 \ No newline at end of file From 003a7ac3e9442dd0a8fc5824e5af1a4ffe2b4e4b Mon Sep 17 00:00:00 2001 From: Konstantinos Tsilimparis Date: Wed, 9 Apr 2025 16:33:15 +0200 Subject: [PATCH 03/12] ENH: add ch_type in the Neuromag and CTF montages That way we can parse the txt files and select the channel type we want to interpolate to. For example we do not want to interpolate to the ch_type = 'ref' for the CTF. --- mne/channels/data/montages/ctf275.txt | 610 ++++++++++---------- mne/channels/data/montages/neuromag306.txt | 614 ++++++++++----------- 2 files changed, 612 insertions(+), 612 deletions(-) diff --git a/mne/channels/data/montages/ctf275.txt b/mne/channels/data/montages/ctf275.txt index d694ffc58ca..cca4d274aa7 100644 --- a/mne/channels/data/montages/ctf275.txt +++ b/mne/channels/data/montages/ctf275.txt @@ -1,305 +1,305 @@ -Name x y z ex ey ez -MLC11 0.086 0.0103 0.1355 0.346 0.0418 0.9373 -MLC12 0.0742 0.0286 0.1379 0.2638 0.1842 0.9468 -MLC13 0.0659 0.0488 0.1335 0.2456 0.3738 0.8944 -MLC14 0.0535 0.0678 0.1269 0.2278 0.5748 0.786 -MLC15 0.0403 0.0822 0.1182 0.1537 0.6329 0.7588 -MLC16 0.0243 0.0921 0.1072 0.1428 0.8536 0.5009 -MLC17 0.0065 0.0961 0.0911 -0.1102 0.9547 0.2762 -MLC21 0.053 0.0316 0.1426 0.2195 0.2189 0.9507 -MLC22 0.0446 0.0513 0.1382 0.1941 0.3723 0.9076 -MLC23 0.032 0.0677 0.1316 0.1201 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-0.822 0.0459 +MRT21 grad 0.0911 -0.0897 0.0339 0.3966 -0.9165 0.0531 +MRT22 grad 0.0618 -0.1008 0.033 0.2988 -0.9532 0.0467 +MRT23 grad 0.0406 -0.107 0.0396 0.0772 -0.9965 0.0325 +MRT24 grad 0.0182 -0.1117 0.0392 -0.0446 -0.9987 0.0249 +MRT25 grad -0.0094 -0.1126 0.0375 -0.1313 -0.9912 0.0195 +MRT26 grad -0.0326 -0.1067 0.0371 -0.3011 -0.9536 0.0092 +MRT27 grad -0.0513 -0.0884 0.037 -0.5075 -0.8617 -0.003 +MRT31 grad 0.0993 -0.0867 0.0144 0.4282 -0.902 0.0552 +MRT32 grad 0.0771 -0.0962 0.019 0.3644 -0.9298 0.051 +MRT33 grad 0.0466 -0.1069 0.019 0.1291 -0.991 0.0358 +MRT34 grad 0.0242 -0.1127 0.0185 -0.0272 -0.9993 0.026 +MRT35 grad 0.0019 -0.1131 0.0192 -0.0793 -0.9966 0.0228 +MRT36 grad -0.021 -0.1112 0.0187 -0.1989 -0.98 -0.0021 +MRT37 grad -0.0426 -0.097 0.0185 -0.398 -0.9173 -0.0141 +MRT41 grad 0.0848 -0.0938 -0.0016 0.3806 -0.9233 0.052 +MRT42 grad 0.062 -0.1017 0.004 0.2822 -0.9583 0.0456 +MRT43 grad 0.0355 -0.1123 0.0002 0.025 -0.9993 0.0293 +MRT44 grad 0.0132 -0.1131 -0.0002 -0.0446 -0.9987 0.0249 +MRT45 grad -0.0093 -0.1129 0.0004 -0.1485 -0.9887 0.0185 +MRT46 grad -0.0332 -0.1064 0 -0.3167 -0.9485 -0.0092 +MRT47 grad -0.0515 -0.0884 0 -0.5224 -0.8527 -0.0039 +MRT51 grad 0.0695 -0.1003 -0.0166 0.3318 -0.9421 0.0489 +MRT52 grad 0.048 -0.1095 -0.018 0.1118 -0.9931 0.0347 +MRT53 grad 0.0247 -0.1134 -0.0195 -0.0272 -0.9993 0.026 +MRT54 grad 0.0017 -0.1139 -0.0189 -0.0956 -0.9954 0.0043 +MRT55 grad -0.0217 -0.1107 -0.0184 -0.2339 -0.9722 0.0133 +MRT56 grad -0.0423 -0.0962 -0.0186 -0.4297 -0.9028 -0.0159 +MRT57 grad -0.0603 -0.0813 -0.0186 -0.6214 -0.783 -0.0271 +MZC01 grad 0.0681 -0.0007 0.1413 0.2659 -0.0067 0.964 +MZC02 grad 0.0314 -0.001 0.1495 0.1636 0.0005 0.9865 +MZC03 grad -0.0071 -0.0011 0.1521 -0.0476 -0.0166 0.9987 +MZC04 grad -0.0457 -0.0014 0.1402 -0.5235 -0.019 0.8518 +MZF01 grad 0.1513 0 0.0494 0.9952 0.0126 0.0973 +MZF02 grad 0.1424 -0.0001 0.0879 0.9093 0.0094 0.416 +MZF03 grad 0.1067 -0.0004 0.1267 0.5362 -0.0024 0.8441 +MZO01 grad -0.0983 -0.0017 0.0598 -0.9487 -0.0114 0.316 +MZO02 grad -0.0997 -0.0017 0.0186 -0.9996 -0.0096 -0.0276 +MZO03 grad -0.0983 -0.0018 -0.0184 -0.9989 -0.0095 -0.045 +MZP01 grad -0.0851 -0.0016 0.0947 -0.8876 -0.0118 0.4605 +BG1 ref -0.0541 -0.0702 0.2384 -0.7126 0.7004 -0.0394 +BG2 ref -0.0541 -0.0702 0.2384 -0.6987 -0.7137 -0.0489 +BG3 ref -0.0541 -0.0702 0.2384 0.0624 0.0073 -0.998 +BP1 ref -0.0554 0.0644 0.2393 -0.7126 0.7004 -0.0394 +BP2 ref -0.0554 0.0644 0.2393 -0.6987 -0.7137 -0.0489 +BP3 ref -0.0554 0.0644 0.2393 0.0624 0.0073 -0.998 +BR1 ref 0.0789 0.0656 0.2477 -0.7126 0.7004 -0.0394 +BR2 ref 0.0789 0.0656 0.2477 -0.6987 -0.7137 -0.0489 +BR3 ref 0.0789 0.0656 0.2477 0.0624 0.0073 -0.998 +G11 ref -0.026 -0.0978 0.24 -0.7126 0.7004 -0.0394 +G12 ref -0.0541 -0.0703 0.2384 -0.6987 -0.7137 -0.0489 +G13 ref -0.0541 -0.0703 0.2384 0.0624 0.0073 -0.998 +G22 ref -0.0267 -0.0422 0.2403 -0.6987 -0.7137 -0.0489 +G23 ref -0.0541 -0.0703 0.2384 0.0624 0.0073 -0.998 +P11 ref -0.0274 0.0369 0.2408 -0.7126 0.7004 -0.0394 +P12 ref -0.0555 0.0644 0.2393 -0.6987 -0.7137 -0.0489 +P13 ref -0.0555 0.0644 0.2393 0.0624 0.0073 -0.998 +P22 ref -0.0279 0.0925 0.2412 -0.6987 -0.7137 -0.0489 +P23 ref -0.0554 0.0644 0.2393 0.0624 0.0073 -0.998 +Q11 ref 0.1086 -0.0969 0.2484 -0.7126 0.7004 -0.0394 +Q12 ref 0.0806 -0.0693 0.2468 -0.6987 -0.7137 -0.0489 +Q13 ref 0.0806 -0.0693 0.2468 0.0624 0.0073 -0.998 +Q22 ref 0.1078 -0.0409 0.2487 -0.6987 -0.7137 -0.0489 +Q23 ref 0.0803 -0.0689 0.2468 0.0624 0.0073 -0.998 +R11 ref 0.107 0.038 0.2493 -0.7126 0.7004 -0.0394 +R12 ref 0.079 0.0656 0.2477 -0.6987 -0.7137 -0.0489 +R13 ref 0.079 0.0656 0.2477 0.0624 0.0073 -0.998 +R22 ref 0.1067 0.094 0.2497 -0.6987 -0.7137 -0.0489 +R23 ref 0.0792 0.066 0.2477 0.0624 0.0073 -0.998 \ No newline at end of file diff --git a/mne/channels/data/montages/neuromag306.txt b/mne/channels/data/montages/neuromag306.txt index 41fa747f36a..ddc37c6b246 100644 --- a/mne/channels/data/montages/neuromag306.txt +++ b/mne/channels/data/montages/neuromag306.txt @@ -1,307 +1,307 @@ -Name x y z ex ey ez -MEG0113 -0.1064 0.0529 -0.0203 -0.9829 0.1844 -0.0019 -MEG0112 -0.1064 0.0529 -0.0203 -0.9829 0.1844 -0.0019 -MEG0111 -0.1064 0.0529 -0.0203 -0.9829 0.1844 -0.0019 -MEG0122 -0.1019 0.0726 0.0129 -0.9658 0.2572 -0.0325 -MEG0123 -0.1019 0.0726 0.0129 -0.9658 0.2572 -0.0325 -MEG0121 -0.1019 0.0726 0.0129 -0.9658 0.2572 -0.0325 -MEG0132 -0.1083 0.0397 0.0148 -0.9965 0.0816 -0.0188 -MEG0133 -0.1083 0.0397 0.0148 -0.9965 0.0816 -0.0188 -MEG0131 -0.1083 0.0397 0.0148 -0.9965 0.0816 -0.0188 -MEG0143 -0.1096 0.0195 -0.0196 -0.9995 0.0264 0.0197 -MEG0142 -0.1096 0.0195 -0.0196 -0.9995 0.0264 0.0197 -MEG0141 -0.1096 0.0195 -0.0196 -0.9995 0.0264 0.0197 -MEG0213 -0.1073 0.0455 0.0491 -0.9936 0.1035 0.0446 -MEG0212 -0.1073 0.0455 0.0491 -0.9936 0.1035 0.0446 -MEG0211 -0.1073 0.0455 0.0491 -0.9936 0.1035 0.0446 -MEG0222 -0.0988 0.0558 0.0817 -0.9266 0.1772 0.3316 -MEG0223 -0.0988 0.0558 0.0817 -0.9266 0.1772 0.3316 -MEG0221 -0.0988 0.0558 0.0817 -0.9266 0.1772 0.3316 -MEG0232 -0.101 0.02 0.0844 -0.9359 -0.0193 0.3518 -MEG0233 -0.101 0.02 0.0844 -0.9359 -0.0193 0.3518 -MEG0231 -0.101 0.02 0.0844 -0.9359 -0.0193 0.3518 -MEG0243 -0.1081 0.0115 0.0512 -0.9941 -0.0788 0.075 -MEG0242 -0.1081 0.0115 0.0512 -0.9941 -0.0788 0.075 -MEG0241 -0.1081 0.0115 0.0512 -0.9941 -0.0788 0.075 -MEG0313 -0.0861 0.1114 0.0443 -0.8737 0.4845 0.0422 -MEG0312 -0.0861 0.1114 0.0443 -0.8737 0.4845 0.0422 -MEG0311 -0.0861 0.1114 0.0443 -0.8737 0.4845 0.0422 -MEG0322 -0.0887 0.0912 0.0785 -0.8628 0.3815 0.3317 -MEG0323 -0.0887 0.0912 0.0785 -0.8628 0.3815 0.3317 -MEG0321 -0.0887 0.0912 0.0785 -0.8628 0.3815 0.3317 -MEG0333 -0.0702 0.0939 0.1079 -0.7075 0.372 0.6009 -MEG0332 -0.0702 0.0939 0.1079 -0.7075 0.372 0.6009 -MEG0331 -0.0702 0.0939 0.1079 -0.7075 0.372 0.6009 -MEG0343 -0.1002 0.0784 0.0463 -0.9551 0.2926 0.0459 -MEG0342 -0.1002 0.0784 0.0463 -0.9551 0.2926 0.0459 -MEG0341 -0.1002 0.0784 0.0463 -0.9551 0.2926 0.0459 -MEG0413 -0.0807 0.0596 0.1123 -0.7561 0.1942 0.625 -MEG0412 -0.0807 0.0596 0.1123 -0.7561 0.1942 0.625 -MEG0411 -0.0807 0.0596 0.1123 -0.7561 0.1942 0.625 -MEG0422 -0.0525 0.061 0.1356 -0.4822 0.2266 0.8463 -MEG0423 -0.0525 0.061 0.1356 -0.4822 0.2266 0.8463 -MEG0421 -0.0525 0.061 0.1356 -0.4822 0.2266 0.8463 -MEG0432 -0.0535 0.0265 0.1403 -0.4947 0.0523 0.8675 -MEG0433 -0.0535 0.0265 0.1403 -0.4947 0.0523 0.8675 -MEG0431 -0.0535 0.0265 0.1403 -0.4947 0.0523 0.8675 -MEG0443 -0.0828 0.0246 0.1162 -0.7634 -0.0045 0.6459 -MEG0442 -0.0828 0.0246 0.1162 -0.7634 -0.0045 0.6459 -MEG0441 -0.0828 0.0246 0.1162 -0.7634 -0.0045 0.6459 -MEG0513 -0.0637 0.1384 0.0465 -0.6127 0.7845 0.0956 -MEG0512 -0.0637 0.1384 0.0465 -0.6127 0.7845 0.0956 -MEG0511 -0.0637 0.1384 0.0465 -0.6127 0.7845 0.0956 -MEG0523 -0.0331 0.1531 0.0491 -0.2883 0.9494 0.1245 -MEG0522 -0.0331 0.1531 0.0491 -0.2883 0.9494 0.1245 -MEG0521 -0.0331 0.1531 0.0491 -0.2883 0.9494 0.1245 -MEG0532 -0.0336 0.1436 0.0813 -0.2713 0.8806 0.3886 -MEG0533 -0.0336 0.1436 0.0813 -0.2713 0.8806 0.3886 -MEG0531 -0.0336 0.1436 0.0813 -0.2713 0.8806 0.3886 -MEG0542 -0.0672 0.1246 0.0787 -0.687 0.6441 0.3365 -MEG0543 -0.0672 0.1246 0.0787 -0.687 0.6441 0.3365 -MEG0541 -0.0672 0.1246 0.0787 -0.687 0.6441 0.3365 -MEG0613 -0.0357 0.1233 0.1097 -0.2934 0.6735 0.6785 -MEG0612 -0.0357 0.1233 0.1097 -0.2934 0.6735 0.6785 -MEG0611 -0.0357 0.1233 0.1097 -0.2934 0.6735 0.6785 -MEG0622 0.0003 0.0981 0.1339 -0.0032 0.4747 0.8801 -MEG0623 0.0003 0.0981 0.1339 -0.0032 0.4747 0.8801 -MEG0621 0.0003 0.0981 0.1339 -0.0032 0.4747 0.8801 -MEG0633 -0.0182 0.0655 0.1464 -0.1288 0.265 0.9556 -MEG0632 -0.0182 0.0655 0.1464 -0.1288 0.265 0.9556 -MEG0631 -0.0182 0.0655 0.1464 -0.1288 0.265 0.9556 -MEG0642 -0.0367 0.0954 0.1295 -0.3099 0.4849 0.8178 -MEG0643 -0.0367 0.0954 0.1295 -0.3099 0.4849 0.8178 -MEG0641 -0.0367 0.0954 0.1295 -0.3099 0.4849 0.8178 -MEG0713 -0.0183 0.0323 0.1527 -0.1513 0.0736 0.9858 -MEG0712 -0.0183 0.0323 0.1527 -0.1513 0.0736 0.9858 -MEG0711 -0.0183 0.0323 0.1527 -0.1513 0.0736 0.9858 -MEG0723 0.0189 0.0324 0.1527 0.1491 0.1212 0.9814 -MEG0722 0.0189 0.0324 0.1527 0.1491 0.1212 0.9814 -MEG0721 0.0189 0.0324 0.1527 0.1491 0.1212 0.9814 -MEG0733 0.019 -0.0016 0.152 0.1492 -0.1534 0.9768 -MEG0732 0.019 -0.0016 0.152 0.1492 -0.1534 0.9768 -MEG0731 0.019 -0.0016 0.152 0.1492 -0.1534 0.9768 -MEG0743 -0.0182 -0.0021 0.1519 -0.1189 -0.1509 0.9814 -MEG0742 -0.0182 -0.0021 0.1519 -0.1189 -0.1509 0.9814 -MEG0741 -0.0182 -0.0021 0.1519 -0.1189 -0.1509 0.9814 -MEG0813 0.0003 0.1581 0.0501 -0.0112 0.986 0.1666 -MEG0812 0.0003 0.1581 0.0501 -0.0112 0.986 0.1666 -MEG0811 0.0003 0.1581 0.0501 -0.0112 0.986 0.1666 -MEG0822 0.0002 0.148 0.0825 -0.0049 0.907 0.421 -MEG0823 0.0002 0.148 0.0825 -0.0049 0.907 0.421 -MEG0821 0.0002 0.148 0.0825 -0.0049 0.907 0.421 -MEG0913 0.0334 0.1532 0.0491 0.2616 0.9542 0.1453 -MEG0912 0.0334 0.1532 0.0491 0.2616 0.9542 0.1453 -MEG0911 0.0334 0.1532 0.0491 0.2616 0.9542 0.1453 -MEG0923 0.0642 0.1386 0.0467 0.6219 0.778 0.089 -MEG0922 0.0642 0.1386 0.0467 0.6219 0.778 0.089 -MEG0921 0.0642 0.1386 0.0467 0.6219 0.778 0.089 -MEG0932 0.0675 0.1249 0.079 0.6744 0.6573 0.3364 -MEG0933 0.0675 0.1249 0.079 0.6744 0.6573 0.3364 -MEG0931 0.0675 0.1249 0.079 0.6744 0.6573 0.3364 -MEG0942 0.034 0.1436 0.0815 0.2621 0.883 0.3895 -MEG0943 0.034 0.1436 0.0815 0.2621 0.883 0.3895 -MEG0941 0.034 0.1436 0.0815 0.2621 0.883 0.3895 -MEG1013 0.0002 0.1281 0.1115 -0.0277 0.7171 0.6964 -MEG1012 0.0002 0.1281 0.1115 -0.0277 0.7171 0.6964 -MEG1011 0.0002 0.1281 0.1115 -0.0277 0.7171 0.6964 -MEG1023 0.036 0.1235 0.1099 0.2684 0.6789 0.6834 -MEG1022 0.036 0.1235 0.1099 0.2684 0.6789 0.6834 -MEG1021 0.036 0.1235 0.1099 0.2684 0.6789 0.6834 -MEG1032 0.0371 0.0955 0.1298 0.3053 0.4832 0.8205 -MEG1033 0.0371 0.0955 0.1298 0.3053 0.4832 0.8205 -MEG1031 0.0371 0.0955 0.1298 0.3053 0.4832 0.8205 -MEG1043 0.0187 0.0657 0.1464 0.1259 0.2893 0.9489 -MEG1042 0.0187 0.0657 0.1464 0.1259 0.2893 0.9489 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0.1026 -0.0208 0.0531 0.9465 -0.3069 0.0995 +MEG2422 grad 0.1026 -0.0208 0.0531 0.9465 -0.3069 0.0995 +MEG2421 mag 0.1026 -0.0208 0.0531 0.9465 -0.3069 0.0995 +MEG2433 grad 0.0875 -0.0509 0.0556 0.8338 -0.5381 0.1235 +MEG2432 grad 0.0875 -0.0509 0.0556 0.8338 -0.5381 0.1235 +MEG2431 mag 0.0875 -0.0509 0.0556 0.8338 -0.5381 0.1235 +MEG2442 grad 0.0789 -0.0469 0.0892 0.765 -0.522 0.3771 +MEG2443 grad 0.0789 -0.0469 0.0892 0.765 -0.522 0.3771 +MEG2441 mag 0.0789 -0.0469 0.0892 0.765 -0.522 0.3771 +MEG2512 grad 0.0639 -0.0806 0.0248 0.5947 -0.8035 0.0273 +MEG2513 grad 0.0639 -0.0806 0.0248 0.5947 -0.8035 0.0273 +MEG2511 mag 0.0639 -0.0806 0.0248 0.5947 -0.8035 0.0273 +MEG2522 grad 0.0871 -0.0561 0.0223 0.8294 -0.558 0.0273 +MEG2523 grad 0.0871 -0.0561 0.0223 0.8294 -0.558 0.0273 +MEG2521 mag 0.0871 -0.0561 0.0223 0.8294 -0.558 0.0273 +MEG2533 grad 0.0767 -0.0728 -0.0104 0.7119 -0.6982 0.0759 +MEG2532 grad 0.0767 -0.0728 -0.0104 0.7119 -0.6982 0.0759 +MEG2531 mag 0.0767 -0.0728 -0.0104 0.7119 -0.6982 0.0759 +MEG2543 grad 0.0498 -0.0925 -0.0088 0.4216 -0.9012 0.1005 +MEG2542 grad 0.0498 -0.0925 -0.0088 0.4216 -0.9012 0.1005 +MEG2541 mag 0.0498 -0.0925 -0.0088 0.4216 -0.9012 0.1005 +MEG2612 grad 0.1096 0.0067 0.0167 0.9978 -0.0658 -0.011 +MEG2613 grad 0.1096 0.0067 0.0167 0.9978 -0.0658 -0.011 +MEG2611 mag 0.1096 0.0067 0.0167 0.9978 -0.0658 -0.011 +MEG2623 grad 0.1078 -0.0136 -0.0157 0.9751 -0.2184 0.0377 +MEG2622 grad 0.1078 -0.0136 -0.0157 0.9751 -0.2184 0.0377 +MEG2621 mag 0.1078 -0.0136 -0.0157 0.9751 -0.2184 0.0377 +MEG2633 grad 0.0961 -0.0454 -0.0128 0.8783 -0.4746 0.0573 +MEG2632 grad 0.0961 -0.0454 -0.0128 0.8783 -0.4746 0.0573 +MEG2631 mag 0.0961 -0.0454 -0.0128 0.8783 -0.4746 0.0573 +MEG2642 grad 0.1026 -0.0261 0.0198 0.9452 -0.3265 0.0044 +MEG2643 grad 0.1026 -0.0261 0.0198 0.9452 -0.3265 0.0044 +MEG2641 mag 0.1026 -0.0261 0.0198 0.9452 -0.3265 0.0044 \ No newline at end of file From 8bfba64628cceb5336df4a72e39a3893014ec154 Mon Sep 17 00:00:00 2001 From: Konstantinos Tsilimparis Date: Wed, 9 Apr 2025 16:33:53 +0200 Subject: [PATCH 04/12] ENH: allow make_standard_montage to accept and parse the new meg montages --- mne/channels/_standard_montage_utils.py | 47 +++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/mne/channels/_standard_montage_utils.py b/mne/channels/_standard_montage_utils.py index eb3dc10d10e..3dcfeb0e512 100644 --- a/mne/channels/_standard_montage_utils.py +++ b/mne/channels/_standard_montage_utils.py @@ -118,6 +118,51 @@ def _mgh_or_standard(basename, head_size, coord_frame="unknown"): ) +def _meg(basename, head_size): + fname = op.join(MONTAGE_PATH, basename) + # Create a simple class instance instead of a list + class CustomMontage: + pass + + montage = CustomMontage() + + # Read the file + with open(fname) as f: + # Skip header line + header = f.readline().strip().split() + + ch_names = [] + ch_types = [] + pos = [] + ori = [] + + for line in f: + parts = line.strip().split() + ch_names.append(parts[0]) + ch_types.append(parts[1]) + pos.append([float(parts[2]), float(parts[3]), float(parts[4])]) + ori.append([float(parts[5]), float(parts[6]), float(parts[7])]) + + pos = np.array(pos) + + montage.ch_names = ch_names + + # # Create a dictionary mapping channel names to positions + # montage.ch_pos = dict(zip(ch_names, pos)) + montage.ch_pos = pos + # # TODO - make_dig_montage(): + # For custom montages without fiducials, this parameter must be set + # to ``'head'``. -> + # "kind": FIFF.FIFFV_POINT_EEG, -> + # dig names each chennel as EEG #1 ... + + # These aren't standard DigMontage attributes but can be useful + montage.ch_types = ch_types + montage.ori = ori + + return montage + + standard_montage_look_up_table = { "EGI_256": _egi_256, "easycap-M1": partial(_easycap, basename="easycap-M1.txt"), @@ -165,6 +210,8 @@ def _mgh_or_standard(basename, head_size, coord_frame="unknown"): "brainproducts-RNP-BA-128": partial( _easycap, basename="brainproducts-RNP-BA-128.txt" ), + "ctf275": partial(_meg, basename="ctf275.txt"), + "neuromag306": partial(_meg, basename="neuromag306.txt"), } From 1857f143b7c950516205350f634df26e537ffe76 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 9 Apr 2025 14:34:19 +0000 Subject: [PATCH 05/12] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- mne/channels/_standard_montage_utils.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/mne/channels/_standard_montage_utils.py b/mne/channels/_standard_montage_utils.py index 3dcfeb0e512..acca4a36736 100644 --- a/mne/channels/_standard_montage_utils.py +++ b/mne/channels/_standard_montage_utils.py @@ -120,10 +120,11 @@ def _mgh_or_standard(basename, head_size, coord_frame="unknown"): def _meg(basename, head_size): fname = op.join(MONTAGE_PATH, basename) + # Create a simple class instance instead of a list class CustomMontage: pass - + montage = CustomMontage() # Read the file @@ -152,8 +153,8 @@ class CustomMontage: montage.ch_pos = pos # # TODO - make_dig_montage(): # For custom montages without fiducials, this parameter must be set - # to ``'head'``. -> - # "kind": FIFF.FIFFV_POINT_EEG, -> + # to ``'head'``. -> + # "kind": FIFF.FIFFV_POINT_EEG, -> # dig names each chennel as EEG #1 ... # These aren't standard DigMontage attributes but can be useful From 73a5042e76aedac346913e25bafff5373425dc03 Mon Sep 17 00:00:00 2001 From: Konstantinos Tsilimparis Date: Wed, 9 Apr 2025 16:34:40 +0200 Subject: [PATCH 06/12] ENH: add neuromag and ctf to the builtin standard montages --- mne/channels/montage.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/mne/channels/montage.py b/mne/channels/montage.py index 15cef38dec7..32ed92cc324 100644 --- a/mne/channels/montage.py +++ b/mne/channels/montage.py @@ -186,6 +186,15 @@ class _BuiltinStandardMontage: name="brainproducts-RNP-BA-128", description="Brain Products with 10-10 electrode names (128 channels)", ), + _BuiltinStandardMontage( + name="ctf275", + description="CTF system with 275 sensors (275 axial gradiometers)", + ), + _BuiltinStandardMontage( + name="neuromag306", + description="Neuromag system with 306 sensors (204 gradiometers, " + "102 magnetometers)", + ), ] From 61ba5a2f837dc26cb1e9e0561f463447eea34047 Mon Sep 17 00:00:00 2001 From: Konstantinos Tsilimparis Date: Wed, 9 Apr 2025 16:42:25 +0200 Subject: [PATCH 07/12] ENH: extend the initial setup/configuration of the function to MEG --- mne/channels/channels.py | 23 +++++++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/mne/channels/channels.py b/mne/channels/channels.py index d0e57eecb5f..55f9b70f153 100644 --- a/mne/channels/channels.py +++ b/mne/channels/channels.py @@ -960,7 +960,7 @@ def interpolate_bads( return self - def interpolate_to(self, sensors, origin="auto", method="spline", reg=0.0): + def interpolate_to(self, sensors, origin="auto", method=None, reg=0.0): """Interpolate EEG data onto a new montage. .. warning:: @@ -1003,8 +1003,27 @@ def interpolate_to(self, sensors, origin="auto", method="spline", reg=0.0): from .montage import DigMontage # Check that the method option is valid. - _check_option("method", method, ["spline", "MNE"]) _validate_type(sensors, DigMontage, "sensors") + method = _handle_default("interpolation_method", method) + + # Filter method to only include 'eeg' and 'meg' + supported_ch_types = ['eeg', 'meg'] + keys_to_delete = [key for key in method if key not in supported_ch_types] + for key in keys_to_delete: + del method[key] + # otherwise when method = "spline", the _handle_default function + # forces all channel types to use that method + # TODO: Check if there is a better way to handle this + if 'meg' in method: + method['meg'] = 'MNE' + valids = { + "eeg": ("spline", "MNE"), + "meg": ("MNE") + } + for key in method: + _check_option("method[key]", key, tuple(valids)) + _check_option(f"method['{key}']", method[key], valids[key]) + logger.info("Setting channel interpolation method to %s.", method) # Get target positions from the montage ch_pos = sensors.get_positions().get("ch_pos", {}) From cb614d9009f66301ea817a4fdd96144f2a020330 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 9 Apr 2025 14:43:03 +0000 Subject: [PATCH 08/12] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- mne/channels/channels.py | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/mne/channels/channels.py b/mne/channels/channels.py index 55f9b70f153..39a03a9f601 100644 --- a/mne/channels/channels.py +++ b/mne/channels/channels.py @@ -1007,19 +1007,16 @@ def interpolate_to(self, sensors, origin="auto", method=None, reg=0.0): method = _handle_default("interpolation_method", method) # Filter method to only include 'eeg' and 'meg' - supported_ch_types = ['eeg', 'meg'] + supported_ch_types = ["eeg", "meg"] keys_to_delete = [key for key in method if key not in supported_ch_types] for key in keys_to_delete: del method[key] - # otherwise when method = "spline", the _handle_default function - # forces all channel types to use that method + # otherwise when method = "spline", the _handle_default function + # forces all channel types to use that method # TODO: Check if there is a better way to handle this - if 'meg' in method: - method['meg'] = 'MNE' - valids = { - "eeg": ("spline", "MNE"), - "meg": ("MNE") - } + if "meg" in method: + method["meg"] = "MNE" + valids = {"eeg": ("spline", "MNE"), "meg": ("MNE")} for key in method: _check_option("method[key]", key, tuple(valids)) _check_option(f"method['{key}']", method[key], valids[key]) From aad0c4ecc3b7f19036a574dd9d9f5b470a1ad650 Mon Sep 17 00:00:00 2001 From: Konstantinos Tsilimparis Date: Wed, 9 Apr 2025 16:43:31 +0200 Subject: [PATCH 09/12] COS: comment --- mne/channels/channels.py | 1 + 1 file changed, 1 insertion(+) diff --git a/mne/channels/channels.py b/mne/channels/channels.py index 55f9b70f153..79fa800367e 100644 --- a/mne/channels/channels.py +++ b/mne/channels/channels.py @@ -1011,6 +1011,7 @@ def interpolate_to(self, sensors, origin="auto", method=None, reg=0.0): keys_to_delete = [key for key in method if key not in supported_ch_types] for key in keys_to_delete: del method[key] + # Force MEG to always use MNE method, # otherwise when method = "spline", the _handle_default function # forces all channel types to use that method # TODO: Check if there is a better way to handle this From d4c043c6631d987f4f155a6bc4f4d97e87815085 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 9 Apr 2025 14:46:34 +0000 Subject: [PATCH 10/12] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- mne/channels/channels.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/mne/channels/channels.py b/mne/channels/channels.py index 70d0d4c6fdd..5126dab4227 100644 --- a/mne/channels/channels.py +++ b/mne/channels/channels.py @@ -1012,9 +1012,9 @@ def interpolate_to(self, sensors, origin="auto", method=None, reg=0.0): for key in keys_to_delete: del method[key] - # Force MEG to always use MNE method, - # otherwise when method = "spline", the _handle_default function - # forces all channel types to use that method + # Force MEG to always use MNE method, + # otherwise when method = "spline", the _handle_default function + # forces all channel types to use that method # TODO: Check if there is a better way to handle this if "meg" in method: method["meg"] = "MNE" From 10f8b7f80c4c2a07cbe9ac463e230d4a8734f32e Mon Sep 17 00:00:00 2001 From: Konstantinos Tsilimparis Date: Wed, 9 Apr 2025 17:05:59 +0200 Subject: [PATCH 11/12] ENH: add example and TODOs --- examples/preprocessing/interpolate_to.py | 17 +++++++++++++++++ mne/channels/channels.py | 3 +++ 2 files changed, 20 insertions(+) diff --git a/examples/preprocessing/interpolate_to.py b/examples/preprocessing/interpolate_to.py index b97a7251cbb..1fa539aabb4 100644 --- a/examples/preprocessing/interpolate_to.py +++ b/examples/preprocessing/interpolate_to.py @@ -29,6 +29,23 @@ print(__doc__) ylim = (-10, 10) +# %% +# Load the MEG data +data_path = sample.data_path() +raw_meg = mne.io.read_raw_fif(fif_file_path) + +raw_meg.pick("meg") + +# %% +# Define the target montage +standard_montage_meg = make_standard_montage("ctf275") + +# %% +# Use interpolate_to to project MEG data to the standard montage +raw_meg_interpolated_mne = raw_meg.copy().interpolate_to( + standard_montage_meg, method="MNE" +) + # %% # Load EEG data data_path = sample.data_path() diff --git a/mne/channels/channels.py b/mne/channels/channels.py index 70d0d4c6fdd..50156dfc65e 100644 --- a/mne/channels/channels.py +++ b/mne/channels/channels.py @@ -1004,6 +1004,8 @@ def interpolate_to(self, sensors, origin="auto", method=None, reg=0.0): # Check that the method option is valid. _validate_type(sensors, DigMontage, "sensors") + # TODO: Handle the error: sensors must be an instance of DigMontage, got .CustomMontage'> instead. + method = _handle_default("interpolation_method", method) # Filter method to only include 'eeg' and 'meg' @@ -1025,6 +1027,7 @@ def interpolate_to(self, sensors, origin="auto", method=None, reg=0.0): logger.info("Setting channel interpolation method to %s.", method) # Get target positions from the montage + # TODO: handle the error: AttributeError: 'CustomMontage' object has no attribute 'get_positions' ch_pos = sensors.get_positions().get("ch_pos", {}) target_ch_names = list(ch_pos.keys()) if not target_ch_names: From f36d9b124fde73dd402db8521b37922c2a0674de Mon Sep 17 00:00:00 2001 From: Konstantinos Tsilimparis Date: Wed, 9 Apr 2025 17:52:38 +0200 Subject: [PATCH 12/12] ENH: added missing line in example --- examples/preprocessing/interpolate_to.py | 1 + 1 file changed, 1 insertion(+) diff --git a/examples/preprocessing/interpolate_to.py b/examples/preprocessing/interpolate_to.py index 1fa539aabb4..aa39e16b422 100644 --- a/examples/preprocessing/interpolate_to.py +++ b/examples/preprocessing/interpolate_to.py @@ -32,6 +32,7 @@ # %% # Load the MEG data data_path = sample.data_path() +fif_file_path = data_path / "MEG" / "sample" / "sample_audvis_raw.fif" raw_meg = mne.io.read_raw_fif(fif_file_path) raw_meg.pick("meg")