Data/sub-005/MRS/all_parameters.csv

+parameter,mean,std
+Ala,0.04139192381102556,0.009661572074995767
+Asc,0.03695350723115995,0.014661670099029894
+Asp,0.06416804292473298,0.02162420898825048
+Cr,0.2229290561673066,0.01357414248931729
+GABA,0.05025729926474188,0.014284309527474203
+GPC,0.07469911051235062,0.004393381651178706
+GSH,0.06861669616329763,0.008385312383754336
+Glc,0.07303282573135256,0.016418794957875227
+Gln,0.04677607914442284,0.016272345199826645
+Glu,0.41091543249344303,0.014675732051883435
+Ins,0.3126591309245602,0.010716564583507804
+Lac,0.041611841320509255,0.009378890835176658
+Mac,0.027426069776383177,0.0005902888657413123
+NAA,0.6203669587379067,0.009499281844355488
+NAAG,0.09768464449536668,0.007170011604595953
+PCh,0.004477933455525159,0.0034795266397417723
+PCr,0.22941643298255576,0.012255344972249517
+PE,0.07936623238202856,0.01791669530655046
+Scyllo,0.008634883087727864,0.0037368865634965945
+Tau,0.06469085128489672,0.012299719221044916
+gamma_0,21.22729626635268,0.9261745144308022
+gamma_1,3.899041009769456,2.9710893866052306
+sigma_0,7.913528876074015,0.8421183792181637
+sigma_1,9.493502017847224,5.499890046335926
+eps_0,-0.5646522264474001,0.3847938780634869
+eps_1,-0.07028988439657347,4.826457977447859
+Phi0,0.0006401349939650235,0.011341158668759108
+Phi1,0.00035571598642902,1.5280168246380067e-05
+B_real_0,0.2623042224756872,0.0
+B_imag_0,-0.21341658134512137,5.607473066727768e-17
+B_real_1,-0.09890354793973166,0.0
+B_imag_1,-0.003471247806565505,4.380838333381069e-19
+B_real_2,0.1372841414317492,2.803736533363884e-17
+B_imag_2,0.046348611270348845,7.00934133340971e-18

Data/sub-005/MRS/concentrations.csv

+Metabs,mean,mean,mean,mean,std,std,std,std
+,raw,internal,molality,molarity,raw,internal,molality,molarity
+Ala,0.04139192381102556,0.09150511015113137,1.0236775231866426,0.7330384602836432,0.009661572074995767,0.027735751012785914,0.2389435730741853,0.17110352130788922
+Asc,0.03695350723115995,0.08169310431416112,0.9139095570469024,0.654435444133535,0.014661670099029894,0.03692756973813724,0.362602671025324,0.25965374607006725
+Asp,0.06416804292473298,0.1418562679719219,1.586961349001799,1.1363966458701196,0.02162420898825048,0.05097406015980383,0.5347955509153253,0.3829582054211387
+Cr,0.2229290561673066,0.49282917927683817,5.513333110718974,3.948006206028028,0.01357414248931729,0.03483637860126211,0.335706661673588,0.24039396079941194
+GABA,0.05025729926474188,0.11110379227876327,1.2429300911033478,0.8900415800733439,0.014284309527474203,0.036197544817050425,0.35327004041356375,0.2529708044023196
+GPC,0.07469911051235062,0.16513729506342606,1.8474087066511184,1.3228986699078118,0.004393381651178706,0.020184244768372456,0.10865419224351891,0.07780546117454437
+GSH,0.06861669616329763,0.1516909039863662,1.6969824813744157,1.2151809501518314,0.008385312383754336,0.02562630604271493,0.20737996743851367,0.14850134791626507
+Glc,0.07303282573135256,0.16145363993484352,1.806199259964774,1.2933892700588603,0.016418794957875227,0.04038002030434497,0.4060587140844616,0.29077189624193733
+Gln,0.04677607914442284,0.10340786028912048,1.156834871013905,0.8283902239160984,0.016272345199826645,0.04008925128728785,0.402436816095982,0.28817831529027715
+Glu,0.41091543249344303,0.908410589582129,10.162487109671588,7.277188113241204,0.014675732051883435,0.03695485861129478,0.3629504418884035,0.25990277900497993
+Ins,0.3126591309245602,0.6911954212523959,7.732477625533488,5.537098709712835,0.010716564583507804,0.02956925048874369,0.26503494594742183,0.18978711976978158
+Lac,0.041611841320509255,0.0919912817053056,1.0291163767282523,0.7369331329081226,0.009378890835176658,0.027257423710524233,0.23195248870829568,0.16609732198905314
+Mac,0.027426069776383177,0.06063080197379154,0.6782833121651985,0.4857074064085054,0.0005902888657413123,0.017741899716545117,0.014598631530283235,0.010453837401738024
+NAA,0.6203669587379067,1.3714449986089694,15.34250291643827,10.98651133782163,0.009499281844355488,0.027460418326943375,0.23492991905564517,0.1682294103742984
+NAAG,0.09768464449536668,0.21595140625576942,2.4158716416980917,1.7299655295356144,0.007170011604595953,0.023755381005294417,0.1773239570627827,0.12697873843324137
+PCh,0.004477933455525159,0.009899365778889455,0.11074527121944425,0.07930284807434869,0.0034795266397417723,0.01929357061238008,0.08605333805441563,0.061621365128064355
+PCr,0.22941643298255576,0.5071708207231617,5.673774598303171,4.062895688663366,0.012255344972249517,0.03235887209857771,0.3030910388284129,0.21703845536915348
+PE,0.07936623238202856,0.1754548995971848,1.962832859869373,1.405551987615976,0.01791669530655046,0.04338087079320414,0.4431037890104989,0.3172992586874283
+Scyllo,0.008634883087727864,0.019089132742223767,0.21355218405907858,0.15292116965269592,0.0037368865634965945,0.019527376614594832,0.09241819247673323,0.06617913159258657
+Tau,0.06469085128489672,0.14301204021394495,1.5998910975604088,1.1456554239135737,0.012299719221044916,0.03244105038362159,0.30418847322908316,0.21782430990352422
+Cr+PCr,0.4523454891498624,0.9999999999999999,11.187107709022147,8.010901894691393,0.008003730416576574,0.02502287383471766,0.1979429360785659,0.14174364660793684

Data/sub-005/MRS/options.txt

+{"data": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/preproc/metab.nii.gz", "basis": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized", "output": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized", "algo": "MH", "ignore": null, "keep": null, "combine": null, "ppmlim": [0.2, 4.2], "h2o": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/preproc/wref.nii.gz", "baseline_order": 2, "metab_groups": ["Mac"], "lorentzian": false, "free_shift": false, "ind_scale": null, "disable_MH_priors": false, "mh_samples": 500, "t1": "/home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRI/MRI.anat/T1_biascorr.nii.gz", "TE": 26.0, "TR": null, "tissue_frac": {"CSF": 0.08002110112222334, "GM": 0.31135867002869877, "WM": 0.608620228849078}, "internal_ref": ["Cr", "PCr"], "wref_metabolite": null, "ref_protons": null, "ref_int_limits": null, "h2o_scale": 1.0, "report": true, "verbose": false, "overwrite": true, "conjfid": null, "conjbasis": null, "no_rescale": false, "config": null}
+--------
+Command Line Args:   --data /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/preproc/metab.nii.gz --basis /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/BasicSpectra_optimization_FHK_SMA_together/slaser_dkd_26_res_50_conj_optimized --output /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/fit_long_slaser_dkd_26_res_50_optimized --algo MH --metab_groups Mac --overwrite --TE 26 --report --t1 /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRI/MRI.anat/T1_biascorr.nii.gz --h2o /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/preproc/wref.nii.gz --tissue_frac /home/fs0/pjs942/scratch/STR7THS_analyzedData_230223/STR7T_HS_006/MRS/FHK/segmentation.json
+Defaults:
+  --ppmlim:          (0.2, 4.2)
+  --baseline_order:  2
+  --mh_samples:      500
+  --internal_ref:    ['Cr', 'PCr']
+  --h2o_scale:       1.0

Data/sub-005/MRS/qc.csv

+Metab,SNR,FWHM
+Ala,15.280636157794806,18.341222561675778
+Asc,10.886125240871396,15.519414832070975
+Asp,6.335592049747118,22.75348210624978
+Cr,137.88505076010384,9.980885629683193
+GABA,10.393492750717419,21.580970036274397
+GPC,139.07471562922458,9.983527251123986
+GSH,36.25555302373578,10.970122900428661
+Glc,13.795320689448536,41.45595934732467
+Gln,8.899759382019143,24.635961230541767
+Glu,93.54148461823348,21.57952933887058
+Ins,93.30731555233187,41.99623174689981
+Lac,15.938860226015816,17.75382651357546
+Mac,84.0924258498793,34.326588323152194
+NAA,369.6840839072808,10.371563847245843
+NAAG,67.41258709805024,10.769625850288595
+PCh,8.078691200989322,10.428035497828803
+PCr,141.02278640915887,10.147073611690494
+PE,19.078956382763632,18.603879366710824
+Scyllo,10.360900904672672,10.672960308394613
+Tau,18.579221861148927,18.804844869498478