All input logs of the command are as follows:
dwi2response:
dwi2response: Note that this script makes use of commands / algorithms that have relevant articles for citation. Please consult the help page (-help option) for more information.
dwi2response:
dwi2response: [DEBUG] path.script_subdir_name() (from algorithm.py:69): dwi2response
dwi2response: [DEBUG] path.from_user() (from dwi2response:83): DWI.mif -> /home/zzc/SC_Martix/DWI.mif
dwi2response: [DEBUG] path.name_temporary() (from image.py:36): /home/zzc/SC_Martix/mrtrix-tmp-ZmYOTG.json
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrinfo -> mrinfo
dwi2response: [DEBUG] run.version_match() (from image.py:37): Version-matched executable for mrinfo: /home/zzc/mrtrix3/bin/mrinfo
dwi2response: [DEBUG] run.exe_name() (from image.py:37): /home/zzc/mrtrix3/bin/mrinfo -> /home/zzc/mrtrix3/bin/mrinfo
dwi2response: Loading header for image file '/home/zzc/SC_Martix/DWI.mif'
dwi2response: [DEBUG] image.__init__() (from dwi2response:83): ['/home/zzc/mrtrix3/bin/mrinfo', '/home/zzc/SC_Martix/DWI.mif', '-json_all', '/home/zzc/SC_Martix/mrtrix-tmp-ZmYOTG.json']
dwi2response: [DEBUG] image.__init__() (from dwi2response:83): {'_name': '/home/zzc/SC_Martix/DWI.mif', '_size': [145, 174, 145, 288], '_spacing': [1.25, 1.25, 1.25, 1.0], '_strides': [-2, 3, 4, 1], '_format': 'MRtrix', '_datatype': 'Float32LE', '_intensity_offset': 0.0, '_intensity_scale': 1.0, '_transform': [[1.0, 0.0, 0.0, -90.0], [-0.0, 1.0, 0.0, -126.0], [-0.0, 0.0, 1.0, -72.0], [0.0, 0.0, 0.0, 1.0]], '_keyval': {'command_history': "mrconvert data.nii.gz DWI.mif -fslgrad bvecs bvals -datatype float32 -strides '0,0,0,1' (version=3.0.3-120-gbb1c2fd4)", 'comments': 'FSL5.0', 'dw_scheme': [[0.5421861165, 0.6720491444, -0.5043651084, 5.0], [-0.918106027, -0.306174009, -0.2516720074, 1000.0], [0.382921085, -0.8436871872, -0.3762490835, 1995.0], [-0.0979770808, -0.442573365, 0.8913637351, 3005.0], [-0.2044101627, 0.9072387222, -0.3676062926, 995.0], [0.420482044, 0.7907960827, 0.4447880465, 2995.0], [0.7131980978, 0.5207080714, -0.4692670643, 2005.0], [-0.3379161867, 0.2872331587, 0.8962754952, 990.0], [-0.5955294942, 0.09847708171, -0.7972746616, 1990.0], [-0.9028822383, 0.4170351101, 0.1043330275, 3000.0], [-0.1726800317, -0.8744021607, -0.4534340834, 1000.0], [-0.2588741056, 0.07737003157, 0.9628073928, 1985.0], [-0.8455802769, -0.4609281509, 0.2693310882, 2995.0], [-0.4098992581, 0.2776821749, -0.8688355471, 1005.0], [-0.9767886981, 0.2054419365, -0.06064198126, 1995.0], [-0.2932492746, 0.9478218877, -0.1250541171, 2995.0], [0.5427522917, 0.6702483602, -0.506149272, 5.0], [-0.9028998279, 0.288457945, 0.3186909393, 995.0], [-0.4248870744, -0.8828291546, -0.2002090351, 2000.0], [-0.1041179932, 0.3826929751, 0.9179899402, 3010.0], [-0.7540533656, 0.08121803938, -0.651772316, 3005.0], [-0.5429951472, -0.6098581653, 0.5772601565, 995.0], [-0.1883340721, 0.796174305, -0.5750102202, 2005.0], [-0.7919474318, 0.5424072957, -0.2803811529, 995.0], [-0.304833999, -0.5444029982, -0.7814739974, 1990.0], [-0.6979992814, 0.1031990416, 0.7086232857, 2985.0], [-0.4381561898, -0.3917891698, -0.8090243505, 1005.0], [-0.7930258356, 0.2511609479, 0.5550028849, 2000.0], [-0.3077471737, -0.8943835048, 0.3246071832, 3005.0], [-0.4866070528, 0.8074630877, 0.3334920362, 995.0], [-0.8674700801, -0.4296370397, -0.2508140232, 1995.0], [-0.5161894045, 0.6013524713, -0.6098554779, 2990.0], [-0.5432390497, -0.6685600611, 0.5078570464, 5.0], [-0.2990738685, 0.7933196512, 0.5302817668, 3005.0], [-0.59307625, -0.8033923387, 0.05311602239, 995.0], [-0.6197003964, 0.7538024821, -0.2185251398, 2000.0], [-0.220479205, -0.2891592688, 0.931544866, 990.0], [-0.2357622701, -0.5209065968, 0.8204099399, 1990.0], [-0.844673202, -0.3773720902, -0.3796280908, 2990.0], [-0.9004208634, -0.2148139674, 0.3782819426, 995.0], [-0.284420182, -0.03824402448, -0.9579366131, 2985.0], [-0.03179001834, -0.995056574, 0.09408405427, 1995.0], [-0.5713793411, -0.4229172524, 0.7033254198, 3005.0], [-0.8334201234, 0.09742801443, -0.5439840806, 995.0], [-0.2442019146, 0.5622108035, 0.7901167238, 2005.0], [0.00376600042, -0.9993481115, -0.03590500401, 1000.0], [-0.7958612216, 0.3472060967, -0.4960371381, 1990.0], [-0.9998933015, -0.009909002987, -0.01073300324, 2995.0], [-0.5434583103, -0.6683413816, 0.50791029, 5.0], [-0.04043200944, 0.5962941392, 0.8017471872, 1005.0], [-0.9487772653, -0.1972710552, 0.246791069, 2005.0], [-0.07464704312, -0.9753695635, -0.2075621199, 2995.0], [-0.6435779148, 0.7495779008, 0.1547269795, 3000.0], [-0.05808602791, 0.6614513178, -0.7477353593, 1005.0], [-0.1663970908, 0.1830860999, -0.9689125287, 1985.0], [-0.6654353292, -0.005058002503, 0.7464383693, 1005.0], [-0.4489089588, -0.4773539562, -0.7553899306, 2985.0], [-0.4421913145, -0.8343875935, 0.329035234, 2005.0], [-0.6495590344, -0.6350160336, -0.4181240221, 995.0], [-0.6784017247, -0.3666648512, -0.6366537417, 1990.0], [-0.05118203121, 0.783971478, -0.6186833773, 3005.0], [-0.5825440022, 0.810136003, -0.06574300025, 1000.0], [-0.5851458794, 0.4768369017, 0.6559198648, 2990.0], [-0.750801238, 0.6078931927, 0.2583860819, 2000.0], [-0.5433284645, -0.6672845704, 0.5094364355, 5.0], [-0.13155201, -0.06543800497, -0.9891470751, 990.0], [-0.6013770686, -0.1570440179, 0.7833790894, 2005.0], [-0.6764463781, -0.7362374116, -0.01935901082, 2995.0], [-0.9922406029, 0.1043119583, -0.06765797292, 1000.0], [-0.06907802356, -0.8705522969, -0.4872031661, 2005.0], [-0.8356672527, 0.4220891277, -0.3514271063, 3000.0], [-0.25822116, -0.876172543, 0.4069932522, 995.0], [-0.4125543062, 0.5235763886, -0.7454305533, 2005.0], [-0.9130912058, -0.0270510061, 0.4068570917, 3005.0], [-0.6141329441, 0.5232519524, 0.5908029462, 1005.0], [0.7575273391, 0.6517092917, -0.03778001691, 2000.0], [-0.2679390448, -0.0508470085, 0.9620931608, 3010.0], [-0.572262235, 0.5422372226, -0.6152192526, 990.0], [-0.1282380946, -0.2524721863, -0.9590687078, 2005.0], [-0.3474301405, 0.9375833792, -0.01515600613, 1995.0], [-0.5413182757, -0.6683583404, 0.5101682598, 5.0], [-0.8475583735, -0.5156732272, 0.1254030553, 1000.0], [-0.3373051548, 0.357488164, -0.8708773996, 3010.0], [-0.5423914475, -0.7000615775, 0.4644623832, 2985.0], [-0.6631098711, -0.149311971, -0.7334788574, 1005.0], [-0.9306989004, -0.04463299522, -0.3630529611, 1995.0], [-0.07822097625, -0.7200017814, -0.6895497906, 3000.0], [-0.1723070412, 0.8390732007, 0.5160101234, 1000.0], [-0.5366201659, 0.3431181061, 0.7709142383, 2005.0], [-0.5601249835, 0.7784279771, -0.2833899917, 3000.0], [-0.5268390943, -0.3252220582, 0.7852841406, 990.0], [-0.1772540954, -0.7990874302, 0.5744913093, 2005.0], [-0.700595847, -0.2451109465, -0.6701388536, 2990.0], [-0.3488169834, -0.9369389554, -0.02172799897, 3000.0], [-0.8283810511, 0.5472810338, 0.1194500074, 1000.0], [-0.5321773213, -0.6773734089, 0.5078903066, 5.0], [-0.8149880733, 0.3897810351, 0.4287950386, 2990.0], [-0.3467462544, -0.9271526802, -0.1419681042, 995.0], [-0.9461798878, 0.1733199794, 0.2733199676, 1995.0], [-0.5173217841, -0.7013397073, -0.4904087954, 1995.0], [-0.1127620779, 0.3515302427, -0.9293606417, 1005.0], [-0.840123462, 0.5251702888, -0.1356050746, 2000.0], [-0.2981441397, 0.9263284341, 0.2302731079, 2995.0], [-0.3376419935, -0.6558819875, -0.6751419871, 1005.0], [-0.1488140212, -0.2557030364, 0.9552331361, 2010.0], [-0.9300779205, -0.3617589691, -0.06391799454, 2995.0], [-0.4723520132, 0.7765530217, -0.4169520117, 1005.0], [-0.04959801979, 0.9731223883, 0.2248840897, 2000.0], [-0.02738900816, 0.113894034, -0.9931152961, 3010.0], [-0.9790637299, -0.1785949507, 0.09766297306, 1000.0], [-0.4598482593, -0.1677780946, -0.8720034916, 2005.0], [-0.9402298112, 0.08243698345, -0.3304119337, 2990.0], [-0.5338801564, -0.6760141981, 0.5079141488, 5.0], [-0.1804770344, 0.04969100946, 0.982323187, 990.0], [-0.2465910514, -0.6743661405, 0.696005145, 2985.0], [-0.806299191, -0.1967980466, 0.5578101321, 2005.0], [-0.3006152256, 0.9505087132, 0.07850905891, 1000.0], [-0.5147232016, 0.7034822756, -0.490074192, 2005.0], [-0.4099311478, 0.2589130934, 0.8745973154, 2985.0], [-0.7426653521, 0.2309981095, 0.628560298, 995.0], [-0.5296338749, 0.6259278522, 0.5724528648, 2005.0], [-0.04223501887, 0.9523864256, -0.3019541349, 2990.0], [-0.7902863099, -0.341599134, -0.5086821995, 995.0], [-0.4687781863, -0.6111902429, 0.6377252535, 2005.0], [-0.7678049935, -0.2464749979, 0.591375995, 2990.0], [-0.2272431062, -0.7131193333, 0.6631903099, 1005.0], [-0.975122361, -0.2116980784, -0.06572902434, 2000.0], [-0.2089061059, -0.380788193, -0.9007544565, 3005.0], [-0.535606357, -0.6732784487, 0.5097273397, 5.0], [-0.6785341538, -0.6582441492, 0.3260460739, 995.0], [-0.6826110385, -0.6416420362, -0.3497680197, 2995.0], [-0.03647299035, -0.6684338231, -0.7428768034, 1990.0], [-0.3361220028, 0.5880450049, 0.7356800061, 1005.0], [-0.9124972359, 0.2688530695, -0.3083290797, 995.0], [-0.1255630791, 0.5406633404, -0.8318155237, 2005.0], [-0.6259573545, 0.3371201909, -0.7032263983, 2990.0], [-0.3429019973, -0.9361199927, 0.07808699939, 2000.0], [-0.7749365551, 0.625351448, -0.09170006569, 3000.0], [-0.202806046, -0.9678072195, 0.1490600338, 1000.0], [-0.7884890127, -0.04305500069, -0.6135400099, 2005.0], [-0.2216580803, 0.6164752233, -0.7555302737, 2985.0], [-0.4374292254, -0.02517201297, -0.8989004631, 990.0], [-0.217475115, 0.9338374939, -0.2839931502, 1995.0], [-0.2431770625, 0.6153621582, 0.7497961927, 2985.0], [-0.5354432019, -0.6752152545, 0.5073311913, 5.0], [-0.1099310426, -0.3739681449, -0.9209033568, 990.0], [-0.6906610753, -0.678676074, -0.2497720272, 2000.0], [-0.4919692753, -0.1815231016, 0.8514784764, 3010.0], [-0.7401728939, -0.3399919513, 0.5801289169, 995.0], [-0.5176009964, 0.07702599947, 0.8521479941, 1990.0], [-0.9689442392, 0.1567680387, 0.1912350472, 2995.0], [-0.332028218, 0.6388334195, -0.6940094557, 1005.0], [-0.5903503163, 0.7955784262, 0.136167073, 2000.0], [-0.5431192339, -0.03841501655, -0.8387763613, 3005.0], [-0.7629140311, -0.6258840255, -0.1619610066, 1000.0], [-0.1328060098, 0.3231490239, 0.9369830693, 1990.0], [-0.1153310777, -0.8818825942, -0.457145308, 2995.0], [-0.8564340231, -0.4709510127, 0.2114850057, 2000.0], [-0.7042972839, 0.6245232518, 0.3375441361, 995.0], [-0.6591140901, -0.7176680981, 0.2247690307, 2990.0], [-0.5364185391, -0.6745306779, 0.5072115097, 5.0], [-0.6871500095, 0.2711840037, -0.6740060093, 995.0], [-0.5848318525, 0.6854428271, 0.4337508906, 3005.0], [-0.6307922664, 0.3917781655, -0.6697842829, 1990.0], [-0.3269962091, 0.8388015364, -0.4352992784, 3005.0], [-0.9532337727, 0.04502798926, 0.2988609287, 1000.0], [-0.8919913584, 0.4145311665, 0.1803200724, 2000.0], [-0.05653501367, 0.9448772285, 0.322507078, 1000.0], [-0.2951920271, -0.7822520719, -0.5485830504, 1990.0], [-0.6160571358, -0.5388101188, -0.5745931267, 2990.0], [-0.08048700603, -0.9954670746, 0.0506670038, 2990.0], [-0.4307461402, -0.04234201378, 0.9014792935, 990.0], [-0.4243622673, -0.3616972279, 0.8301155229, 2010.0], [-0.4617560751, -0.8070251313, -0.3680920599, 995.0], [-0.1038070477, -0.9319564283, 0.3473921597, 2005.0], [-0.9517702876, -0.2386950721, 0.1927640583, 3000.0], [-0.5352792337, -0.6764372954, 0.5058742209, 5.0], [0.01639101429, -0.8579387478, 0.5134904476, 1005.0], [-0.01872300401, 0.1442700309, 0.9893612117, 2980.0], [-0.2182719921, 0.7725609721, 0.5962439785, 2005.0], [-0.9546949744, -0.05029599865, -0.2933049921, 1000.0], [-0.3730261278, 0.09431903232, -0.9230143163, 1985.0], [-0.9287808137, 0.2125999573, -0.3035909391, 2005.0], [-0.9219363253, 0.3864571364, -0.02615900923, 1000.0], [-0.3297462628, -0.4335833455, 0.8386136683, 2985.0], [-0.9482294076, 0.2850621225, -0.1400020602, 2995.0], [-0.1658790771, -0.5239052434, 0.8354683882, 990.0], [-0.6347061926, -0.7229122194, 0.2730310828, 1995.0], [-0.8849112666, -0.1413150426, -0.4438041337, 3005.0], [-0.4914500933, 0.8704181653, 0.02913800553, 2995.0], [-0.3721691597, 0.9157643928, -0.1512140649, 995.0], [-0.5323281903, -0.6764632418, 0.5089441819, 5.0], [-0.8654391642, 0.02754800523, 0.5002560949, 1995.0], [-0.06446101832, -0.7503422132, -0.6578991869, 1005.0], [-0.4994890898, -0.8440671518, -0.1950930351, 3000.0], [-0.7433621122, -0.4863620734, -0.4592000693, 1990.0], [-0.5456509237, 0.279127961, 0.7901598895, 995.0], [0.0115049999, 0.001909999983, 0.9999319911, 2010.0], [-0.8213460136, 0.1738520029, 0.543292009, 2995.0], [-0.4851910952, -0.8232351615, 0.2947430578, 995.0], [-0.7217366201, 0.5802994985, -0.3772913241, 2005.0], [-0.1831080426, -0.8401401954, 0.5105251187, 2990.0], [-0.6018012567, -0.4755992029, -0.6415922737, 995.0], [-0.1866550491, -0.9606312529, -0.2057850542, 2000.0], [-0.2751439157, -0.6341368057, -0.7226107786, 2985.0], [-0.229626216, 0.1471361384, -0.9620929049, 1005.0], [-0.6968494821, 0.5466183782, -0.4643373213, 2990.0], [-0.7120071996, 0.4823811353, 0.5102491431, 1995.0], [-0.5317591962, -0.6780612502, 0.5074101873, 5.0], [-0.1493911097, 0.3114092288, -0.9384596894, 3010.0], [-0.8276541281, -0.04373200677, 0.5595320866, 1005.0], [0.0134330081, 0.6992894217, -0.714712431, 1990.0], [-0.6581536518, 0.6958206892, -0.2875192848, 1000.0], [-0.4965859121, -0.3910759307, -0.7748948628, 2005.0], [-0.7243023855, -0.4844912579, 0.4905652611, 2990.0], [-0.4165110768, 0.721621133, 0.5529751019, 995.0], [-0.9960571119, -0.01895800213, 0.08666500974, 2000.0], [-0.1348669823, 0.8955578821, 0.4240129442, 2995.0], [-0.9078874165, -0.4160747326, -0.05120796709, 1000.0], [-0.4286242696, 0.8660715447, -0.2572961618, 2005.0], [-0.3955669314, 0.4533139214, 0.7987698614, 2990.0], [-0.8249126994, -0.5577347968, -0.0919289665, 3000.0], [-0.3094420878, -0.2425890688, -0.9194542609, 1005.0], [-0.6402392352, -0.394739145, 0.6589952421, 1990.0], [-0.5313663934, -0.6794705031, 0.5059343746, 5.0], [-0.04763104075, 0.9809978394, -0.1880811609, 995.0], [-0.5040972245, 0.1757890783, -0.8455673765, 3010.0], [-0.07061502465, -0.4654791625, -0.882237308, 2005.0], [-0.7659709521, 0.4167049739, -0.4895359694, 995.0], [-0.2707841389, 0.9401534822, 0.2068511061, 2000.0], [-0.7838129947, 0.5548239962, 0.2789399981, 3000.0], [-0.48925288, 0.03418399161, 0.8714717862, 2985.0], [-0.7985143265, -0.4663241907, 0.3806791557, 995.0], [-0.3034030462, 0.3870490589, -0.8707121325, 1990.0], [-0.4729381628, -0.8655742979, 0.1646530567, 2995.0], [-0.1443900483, 0.3932241314, 0.9080343035, 995.0], [-0.5677470109, -0.8231790158, -0.006296000121, 2000.0], [-0.3931679717, -0.5359739614, 0.7470949462, 995.0], [-0.8647940483, -0.2420450135, -0.4399380246, 2005.0], [-0.4316711754, -0.2543701034, -0.8654223517, 3010.0], [-0.5308969881, -0.6797899848, 0.5059979887, 5.0], [-0.968537361, -0.1451060541, -0.2021870754, 2995.0], [-0.6771589905, 0.7248269898, 0.1268129982, 1000.0], [-0.7037823249, 0.04702902171, 0.7088573272, 1990.0], [-0.8344084267, -0.1215850622, -0.5375682749, 995.0], [-0.3490451675, 0.3513751686, 0.8687364168, 1990.0], [-0.1493979878, 0.9873959194, 0.05224499574, 3000.0], [-0.5771878832, -0.7971038387, -0.1774249641, 1000.0], [-0.7587784104, 0.6503483518, 0.03608801952, 2000.0], [-0.00389600318, -0.6291395135, 0.7772826344, 2985.0], [-0.2857350974, 0.4860461658, -0.8259022817, 990.0], [-0.3740271324, -0.7717892733, 0.5142421821, 1990.0], [-0.8258869898, 0.2632029968, -0.4986329939, 2990.0], [-0.7790668242, 0.4065579082, 0.4772478923, 1000.0], [-0.008417998813, -0.5423509235, -0.8401098815, 3005.0], [-0.770621021, 0.1724710047, -0.6135120167, 1990.0], [-0.5302269872, -0.6814309835, 0.5044909878, 5.0], [-0.0559090489, -0.1482061296, 0.9873748637, 1005.0], [-0.896094411, -0.4437997083, -0.007524995054, 2000.0], [-0.3476890255, 0.7270600534, -0.5920270435, 2990.0], [-0.1451460093, -0.9600870617, -0.2390930154, 1000.0], [-0.3398800155, -0.1565240071, 0.9273520423, 1990.0], [-0.289948956, -0.9049838625, -0.3113419527, 3000.0], [-0.9709569389, 0.2024949873, 0.127429992, 1000.0], [-0.5708558403, 0.7266677968, 0.3822008931, 2000.0], [-0.6961588724, -0.125273977, 0.7068728705, 2985.0], [-0.6398370168, 0.07506300197, -0.7648360201, 995.0], [-0.3331021381, 0.689642286, -0.6429902666, 1990.0], [-0.4656779547, 0.8216529201, 0.328679968, 3000.0], [-0.2145559382, -0.5440828432, -0.8111347663, 1005.0], [-0.428309166, -0.6480992511, 0.629697244, 3005.0], [-0.4691451907, -0.5884132392, -0.6585382677, 2005.0], [-0.5298741128, -0.6828371454, 0.5029581071, 5.0], [-0.2693142484, 0.7949527331, -0.5436175013, 995.0], [-0.1564331226, 0.9868927734, -0.03964003106, 1995.0], [-0.8763196623, -0.2762208935, 0.3946718479, 3005.0], [-0.3022632072, 0.8948736134, 0.3283872251, 1000.0], [-0.4128254418, -0.7719168261, 0.4834455174, 995.0], [-0.7300552361, 0.6339292051, -0.2552510826, 2990.0], [-0.2218789924, 0.1634629944, 0.961274967, 2985.0], [-0.8483030104, -0.3487640043, 0.3984290049, 2005.0], [-0.2749470767, -0.093233026, -0.9569282668, 1990.0], [-0.803743729, -0.4862358361, -0.3428858844, 1000.0], [-0.742515057, -0.3882790298, -0.5458120419, 2990.0], [-0.2990059573, -0.8771008748, -0.3758849463, 2000.0], [-0.651566104, -0.2114160338, 0.7285361163, 1005.0], [-0.9878630087, 0.008873000078, -0.1550740014, 1995.0], [-0.46236328, 0.6267413795, 0.6272283798, 3000.0]], 'mrtrix_version': '3.0.3-120-gbb1c2fd4'}}
dwi2response: Generated scratch directory: /home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/
dwi2response: [DEBUG] path.from_user() (from dwi2response:93): DWI.mif -> /home/zzc/SC_Martix/DWI.mif
dwi2response: Importing DWI data (/home/zzc/SC_Martix/DWI.mif)...
dwi2response: [DEBUG] path.from_user() (from dwi2response:94): DWI.mif -> /home/zzc/SC_Martix/DWI.mif
dwi2response: [DEBUG] path.to_scratch() (from dwi2response:94): dwi.mif -> /home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/dwi.mif
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrconvert -> mrconvert
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrconvert: /home/zzc/mrtrix3/bin/mrconvert
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrconvert": Not a text file
dwi2response: [DEBUG] run.command() (from dwi2response:94): To execute: [['/home/zzc/mrtrix3/bin/mrconvert', '/home/zzc/SC_Martix/DWI.mif', '/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/dwi.mif', '-strides', '0,0,0,1']]
Command: mrconvert /home/zzc/SC_Martix/DWI.mif /home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/dwi.mif -strides 0,0,0,1
mrconvert: [INFO] opening image "/home/zzc/SC_Martix/DWI.mif"...
mrconvert: [INFO] image "/home/zzc/SC_Martix/DWI.mif" opened with dimensions 145x174x145x288, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrconvert: [INFO] found 288x4 diffusion gradient table
mrconvert: [INFO] opening image "0,0,0,1"...
mrconvert: [INFO] creating image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/dwi.mif"...
mrconvert: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/dwi.mif" created with dimensions 145x174x145x288, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrconvert: [100%] copying from "/home/zzc/SC_Martix/DWI.mif" to "/home/zzc/...response-tmp-NX2EQ2/dwi.mif"
dwi2response: Changing to scratch directory (/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/)
dwi2response: Computing brain mask (dwi2mask)...
dwi2response: [DEBUG] run.exe_name() (from run.py:561): dwi2mask -> dwi2mask
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for dwi2mask: /home/zzc/mrtrix3/bin/dwi2mask
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/dwi2mask": Not a text file
dwi2response: [DEBUG] run.command() (from dwi2response:113): To execute: [['/home/zzc/mrtrix3/bin/dwi2mask', 'dwi.mif', 'mask.mif']]
Command: dwi2mask dwi.mif mask.mif
dwi2mask: [INFO] opening image "dwi.mif"...
dwi2mask: [INFO] image "dwi.mif" opened with dimensions 145x174x145x288, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
dwi2mask: [INFO] found 288x4 diffusion gradient table
dwi2mask: [INFO] Diffusion gradient encoding data clustered into 3 non-zero shells and 18 b=0 volumes
dwi2mask: [done] computing dwi brain mask
dwi2mask: [INFO] creating image "mask.mif"...
dwi2mask: [INFO] image "mask.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
dwi2mask: [done] applying mask cleaning filter
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrstats -> mrstats
dwi2response: [DEBUG] run.version_match() (from image.py:233): Version-matched executable for mrstats: /home/zzc/mrtrix3/bin/mrstats
dwi2response: [DEBUG] run.exe_name() (from image.py:233): /home/zzc/mrtrix3/bin/mrstats -> /home/zzc/mrtrix3/bin/mrstats
dwi2response: Command: '/home/zzc/mrtrix3/bin/mrstats mask.mif -output mean -output median -output std -output std_rv -output min -output max -output count -mask mask.mif' (piping data to local storage)
dwi2response: Result: ImageStatistics(mean=1.0, median=1.0, std=0.0, std_rv=0.0, min=1.0, max=1.0, count=880236)
dwi2response: -------
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrinfo -> mrinfo
dwi2response: [DEBUG] run.version_match() (from image.py:153): Version-matched executable for mrinfo: /home/zzc/mrtrix3/bin/mrinfo
dwi2response: [DEBUG] run.exe_name() (from image.py:153): /home/zzc/mrtrix3/bin/mrinfo -> /home/zzc/mrtrix3/bin/mrinfo
dwi2response: Command: '/home/zzc/mrtrix3/bin/mrinfo dwi.mif -shell_bvalues' (piping data to local storage)
dwi2response: Result: 5 998.111 1998.28 2996
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrinfo -> mrinfo
dwi2response: [DEBUG] run.version_match() (from image.py:153): Version-matched executable for mrinfo: /home/zzc/mrtrix3/bin/mrinfo
dwi2response: [DEBUG] run.exe_name() (from image.py:153): /home/zzc/mrtrix3/bin/mrinfo -> /home/zzc/mrtrix3/bin/mrinfo
dwi2response: Command: '/home/zzc/mrtrix3/bin/mrinfo dwi.mif -shell_sizes' (piping data to local storage)
dwi2response: Result: 18 90 90 90
dwi2response: 4 unique b-value(s) detected: 5,998,1998,2996 with 18,90,90,90 volumes
dwi2response: -------
dwi2response: Preparation:
dwi2response: * Eroding brain mask by 3 pass(es)...
dwi2response: [DEBUG] run.exe_name() (from run.py:561): maskfilter -> maskfilter
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for maskfilter: /home/zzc/mrtrix3/bin/maskfilter
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/maskfilter": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:110): To execute: [['/home/zzc/mrtrix3/bin/maskfilter', 'mask.mif', 'erode', 'eroded_mask.mif', '-npass', '3']]
Command: maskfilter mask.mif erode eroded_mask.mif -npass 3
maskfilter: [INFO] opening image "mask.mif"...
maskfilter: [INFO] image "mask.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
maskfilter: [INFO] creating image "eroded_mask.mif"...
maskfilter: [INFO] image "eroded_mask.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
maskfilter: [100%] applying erode filter to image mask.mif
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrstats -> mrstats
dwi2response: [DEBUG] run.version_match() (from image.py:233): Version-matched executable for mrstats: /home/zzc/mrtrix3/bin/mrstats
dwi2response: [DEBUG] run.exe_name() (from image.py:233): /home/zzc/mrtrix3/bin/mrstats -> /home/zzc/mrtrix3/bin/mrstats
dwi2response: Command: '/home/zzc/mrtrix3/bin/mrstats mask.mif -output mean -output median -output std -output std_rv -output min -output max -output count -mask mask.mif' (piping data to local storage)
dwi2response: Result: ImageStatistics(mean=1.0, median=1.0, std=0.0, std_rv=0.0, min=1.0, max=1.0, count=880236)
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrstats -> mrstats
dwi2response: [DEBUG] run.version_match() (from image.py:233): Version-matched executable for mrstats: /home/zzc/mrtrix3/bin/mrstats
dwi2response: [DEBUG] run.exe_name() (from image.py:233): /home/zzc/mrtrix3/bin/mrstats -> /home/zzc/mrtrix3/bin/mrstats
dwi2response: Command: '/home/zzc/mrtrix3/bin/mrstats eroded_mask.mif -output mean -output median -output std -output std_rv -output min -output max -output count -mask eroded_mask.mif' (piping data to local storage)
dwi2response: Result: ImageStatistics(mean=1.0, median=1.0, std=0.0, std_rv=0.0, min=1.0, max=1.0, count=728255)
dwi2response: [ mask: 880236 -> 728255 ]
dwi2response: * Computing signal decay metric (SDM):
dwi2response: * b=5...
dwi2response: [DEBUG] run.exe_name() (from run.py:561): dwiextract -> dwiextract
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for dwiextract: /home/zzc/mrtrix3/bin/dwiextract
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/dwiextract": Not a text file
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrmath -> mrmath
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrmath: /home/zzc/mrtrix3/bin/mrmath
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrmath": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:127): To execute: [['/home/zzc/mrtrix3/bin/dwiextract', 'dwi.mif', '-shells', '5', '-'], ['/home/zzc/mrtrix3/bin/mrcalc', '-', '0', '-max', '-'], ['/home/zzc/mrtrix3/bin/mrmath', '-', 'mean', 'mean_b5.mif', '-axis', '3']]
Command: dwiextract dwi.mif -shells 5 - | mrcalc - 0 -max - | mrmath - mean mean_b5.mif -axis 3
dwiextract: [INFO] opening image "dwi.mif"...
dwiextract: [INFO] image "dwi.mif" opened with dimensions 145x174x145x288, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
dwiextract: [INFO] found 288x4 diffusion gradient table
dwiextract: [INFO] Diffusion gradient encoding data clustered into 3 non-zero shells and 18 b=0 volumes
dwiextract: [INFO] creating image "-"...
dwiextract: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-w8YaC9.mif" created with dimensions 145x174x145x18, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
dwiextract: [100%] extracting volumes
mrcalc: [INFO] opening image "-"...
mrcalc: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-w8YaC9.mif" opened with dimensions 145x174x145x18, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] creating image "-"...
mrcalc: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-HtrLdn.mif" created with dimensions 145x174x145x18, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrcalc: [100%] computing: max (/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-w8YaC9.mif, 0)
mrmath: [INFO] opening image "-"...
mrmath: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-HtrLdn.mif" opened with dimensions 145x174x145x18, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrmath: [INFO] creating image "mean_b5.mif"...
mrmath: [INFO] image "mean_b5.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrmath: [100%] computing mean along axis 3...
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:129): To execute: [['/home/zzc/mrtrix3/bin/mrcalc', 'mean_b5.mif', '-finite', 'mean_b5.mif', '0', '-if', '0', '-le', 'err_b5.mif', '-datatype', 'bit']]
Command: mrcalc mean_b5.mif -finite mean_b5.mif 0 -if 0 -le err_b5.mif -datatype bit
mrcalc: [INFO] opening image "mean_b5.mif"...
mrcalc: [INFO] image "mean_b5.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] creating image "err_b5.mif"...
mrcalc: [INFO] image "err_b5.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [100%] computing: ((finite (mean_b5.mif) ? mean_b5.mif : 0) <= 0)
dwi2response: * b=998...
dwi2response: [DEBUG] run.exe_name() (from run.py:561): dwiextract -> dwiextract
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for dwiextract: /home/zzc/mrtrix3/bin/dwiextract
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/dwiextract": Not a text file
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrmath -> mrmath
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrmath: /home/zzc/mrtrix3/bin/mrmath
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrmath": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:127): To execute: [['/home/zzc/mrtrix3/bin/dwiextract', 'dwi.mif', '-shells', '998', '-'], ['/home/zzc/mrtrix3/bin/mrcalc', '-', '0', '-max', '-'], ['/home/zzc/mrtrix3/bin/mrmath', '-', 'mean', 'mean_b998.mif', '-axis', '3']]
Command: dwiextract dwi.mif -shells 998 - | mrcalc - 0 -max - | mrmath - mean mean_b998.mif -axis 3
dwiextract: [INFO] opening image "dwi.mif"...
dwiextract: [INFO] image "dwi.mif" opened with dimensions 145x174x145x288, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
dwiextract: [INFO] found 288x4 diffusion gradient table
dwiextract: [INFO] Diffusion gradient encoding data clustered into 3 non-zero shells and 18 b=0 volumes
dwiextract: [INFO] creating image "-"...
dwiextract: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-vbeZH8.mif" created with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
dwiextract: [100%] extracting volumes
mrcalc: [INFO] opening image "-"...
mrcalc: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-vbeZH8.mif" opened with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] creating image "-"...
mrcalc: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-dV4aEj.mif" created with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrcalc: [100%] computing: max (/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-vbeZH8.mif, 0)
mrmath: [INFO] opening image "-"...
mrmath: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-dV4aEj.mif" opened with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrmath: [INFO] creating image "mean_b998.mif"...
mrmath: [INFO] image "mean_b998.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrmath: [100%] computing mean along axis 3...
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:129): To execute: [['/home/zzc/mrtrix3/bin/mrcalc', 'mean_b998.mif', '-finite', 'mean_b998.mif', '0', '-if', '0', '-le', 'err_b998.mif', '-datatype', 'bit']]
Command: mrcalc mean_b998.mif -finite mean_b998.mif 0 -if 0 -le err_b998.mif -datatype bit
mrcalc: [INFO] opening image "mean_b998.mif"...
mrcalc: [INFO] image "mean_b998.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] creating image "err_b998.mif"...
mrcalc: [INFO] image "err_b998.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [100%] computing: ((finite (mean_b998.mif) ? mean_b998.mif : 0) <= 0)
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:134): To execute: [['/home/zzc/mrtrix3/bin/mrcalc', 'mean_b5.mif', 'mean_b998.mif', '-divide', '-log', 'sdm_b998.mif']]
Command: mrcalc mean_b5.mif mean_b998.mif -divide -log sdm_b998.mif
mrcalc: [INFO] opening image "mean_b5.mif"...
mrcalc: [INFO] image "mean_b5.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "mean_b998.mif"...
mrcalc: [INFO] image "mean_b998.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] creating image "sdm_b998.mif"...
mrcalc: [INFO] image "sdm_b998.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [100%] computing: log ((mean_b5.mif / mean_b998.mif))
dwi2response: * b=1998...
dwi2response: [DEBUG] run.exe_name() (from run.py:561): dwiextract -> dwiextract
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for dwiextract: /home/zzc/mrtrix3/bin/dwiextract
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/dwiextract": Not a text file
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrmath -> mrmath
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrmath: /home/zzc/mrtrix3/bin/mrmath
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrmath": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:127): To execute: [['/home/zzc/mrtrix3/bin/dwiextract', 'dwi.mif', '-shells', '1998', '-'], ['/home/zzc/mrtrix3/bin/mrcalc', '-', '0', '-max', '-'], ['/home/zzc/mrtrix3/bin/mrmath', '-', 'mean', 'mean_b1998.mif', '-axis', '3']]
Command: dwiextract dwi.mif -shells 1998 - | mrcalc - 0 -max - | mrmath - mean mean_b1998.mif -axis 3
dwiextract: [INFO] opening image "dwi.mif"...
dwiextract: [INFO] image "dwi.mif" opened with dimensions 145x174x145x288, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
dwiextract: [INFO] found 288x4 diffusion gradient table
dwiextract: [INFO] Diffusion gradient encoding data clustered into 3 non-zero shells and 18 b=0 volumes
dwiextract: [INFO] creating image "-"...
dwiextract: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-76GK89.mif" created with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
dwiextract: [100%] extracting volumes
mrcalc: [INFO] opening image "-"...
mrcalc: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-76GK89.mif" opened with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] creating image "-"...
mrcalc: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-vWh1ol.mif" created with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrcalc: [100%] computing: max (/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-76GK89.mif, 0)
mrmath: [INFO] opening image "-"...
mrmath: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-vWh1ol.mif" opened with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrmath: [INFO] creating image "mean_b1998.mif"...
mrmath: [INFO] image "mean_b1998.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrmath: [100%] computing mean along axis 3...
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:129): To execute: [['/home/zzc/mrtrix3/bin/mrcalc', 'mean_b1998.mif', '-finite', 'mean_b1998.mif', '0', '-if', '0', '-le', 'err_b1998.mif', '-datatype', 'bit']]
Command: mrcalc mean_b1998.mif -finite mean_b1998.mif 0 -if 0 -le err_b1998.mif -datatype bit
mrcalc: [INFO] opening image "mean_b1998.mif"...
mrcalc: [INFO] image "mean_b1998.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] creating image "err_b1998.mif"...
mrcalc: [INFO] image "err_b1998.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [100%] computing: ((finite (mean_b1998.mif) ? mean_b1998.mif : 0) <= 0)
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:134): To execute: [['/home/zzc/mrtrix3/bin/mrcalc', 'mean_b5.mif', 'mean_b1998.mif', '-divide', '-log', 'sdm_b1998.mif']]
Command: mrcalc mean_b5.mif mean_b1998.mif -divide -log sdm_b1998.mif
mrcalc: [INFO] opening image "mean_b5.mif"...
mrcalc: [INFO] image "mean_b5.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "mean_b1998.mif"...
mrcalc: [INFO] image "mean_b1998.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] creating image "sdm_b1998.mif"...
mrcalc: [INFO] image "sdm_b1998.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [100%] computing: log ((mean_b5.mif / mean_b1998.mif))
dwi2response: * b=2996...
dwi2response: [DEBUG] run.exe_name() (from run.py:561): dwiextract -> dwiextract
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for dwiextract: /home/zzc/mrtrix3/bin/dwiextract
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/dwiextract": Not a text file
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrmath -> mrmath
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrmath: /home/zzc/mrtrix3/bin/mrmath
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrmath": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:127): To execute: [['/home/zzc/mrtrix3/bin/dwiextract', 'dwi.mif', '-shells', '2996', '-'], ['/home/zzc/mrtrix3/bin/mrcalc', '-', '0', '-max', '-'], ['/home/zzc/mrtrix3/bin/mrmath', '-', 'mean', 'mean_b2996.mif', '-axis', '3']]
Command: dwiextract dwi.mif -shells 2996 - | mrcalc - 0 -max - | mrmath - mean mean_b2996.mif -axis 3
dwiextract: [INFO] opening image "dwi.mif"...
dwiextract: [INFO] image "dwi.mif" opened with dimensions 145x174x145x288, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
dwiextract: [INFO] found 288x4 diffusion gradient table
dwiextract: [INFO] Diffusion gradient encoding data clustered into 3 non-zero shells and 18 b=0 volumes
dwiextract: [INFO] creating image "-"...
dwiextract: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-SXZbBS.mif" created with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
dwiextract: [100%] extracting volumes
mrcalc: [INFO] opening image "-"...
mrcalc: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-SXZbBS.mif" opened with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] creating image "-"...
mrcalc: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-H2Gv9m.mif" created with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrcalc: [100%] computing: max (/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-SXZbBS.mif, 0)
mrmath: [INFO] opening image "-"...
mrmath: [INFO] image "/home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/mrtrix-tmp-H2Gv9m.mif" opened with dimensions 145x174x145x90, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mrmath: [INFO] creating image "mean_b2996.mif"...
mrmath: [INFO] image "mean_b2996.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrmath: [100%] computing mean along axis 3...
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:129): To execute: [['/home/zzc/mrtrix3/bin/mrcalc', 'mean_b2996.mif', '-finite', 'mean_b2996.mif', '0', '-if', '0', '-le', 'err_b2996.mif', '-datatype', 'bit']]
Command: mrcalc mean_b2996.mif -finite mean_b2996.mif 0 -if 0 -le err_b2996.mif -datatype bit
mrcalc: [INFO] opening image "mean_b2996.mif"...
mrcalc: [INFO] image "mean_b2996.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] creating image "err_b2996.mif"...
mrcalc: [INFO] image "err_b2996.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [100%] computing: ((finite (mean_b2996.mif) ? mean_b2996.mif : 0) <= 0)
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:134): To execute: [['/home/zzc/mrtrix3/bin/mrcalc', 'mean_b5.mif', 'mean_b2996.mif', '-divide', '-log', 'sdm_b2996.mif']]
Command: mrcalc mean_b5.mif mean_b2996.mif -divide -log sdm_b2996.mif
mrcalc: [INFO] opening image "mean_b5.mif"...
mrcalc: [INFO] image "mean_b5.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "mean_b2996.mif"...
mrcalc: [INFO] image "mean_b2996.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] creating image "sdm_b2996.mif"...
mrcalc: [INFO] image "sdm_b2996.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [100%] computing: log ((mean_b5.mif / mean_b2996.mif))
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:140): To execute: [['/home/zzc/mrtrix3/bin/mrcalc', 'sdm_b998.mif', '90', '-mult', 'sdm_b1998.mif', '90', '-mult', '-add', 'sdm_b2996.mif', '90', '-mult', '-add', '270', '-divide', 'full_sdm.mif']]
Command: mrcalc sdm_b998.mif 90 -mult sdm_b1998.mif 90 -mult -add sdm_b2996.mif 90 -mult -add 270 -divide full_sdm.mif
mrcalc: [INFO] opening image "sdm_b998.mif"...
mrcalc: [INFO] image "sdm_b998.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "90"...
mrcalc: [INFO] opening image "sdm_b1998.mif"...
mrcalc: [INFO] image "sdm_b1998.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "90"...
mrcalc: [INFO] opening image "sdm_b2996.mif"...
mrcalc: [INFO] image "sdm_b2996.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "90"...
mrcalc: [INFO] opening image "270"...
mrcalc: [INFO] creating image "full_sdm.mif"...
mrcalc: [INFO] image "full_sdm.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [100%] computing: ((((sdm_b998.mif * 90) + (sdm_b1998.mif * 90)) + (sdm_b2996.mif * 90)) / 270)
dwi2response: * Removing erroneous voxels from mask and correcting SDM...
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:142): To execute: [['/home/zzc/mrtrix3/bin/mrcalc', 'full_sdm.mif', '-finite', 'full_sdm.mif', '0', '-if', '0', '-le', 'err_sdm.mif', '-datatype', 'bit']]
Command: mrcalc full_sdm.mif -finite full_sdm.mif 0 -if 0 -le err_sdm.mif -datatype bit
mrcalc: [INFO] opening image "full_sdm.mif"...
mrcalc: [INFO] image "full_sdm.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] creating image "err_sdm.mif"...
mrcalc: [INFO] image "err_sdm.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [100%] computing: ((finite (full_sdm.mif) ? full_sdm.mif : 0) <= 0)
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:144): To execute: [['/home/zzc/mrtrix3/bin/mrcalc', 'err_b5.mif', 'err_b998.mif', '-add', 'err_b1998.mif', '-add', 'err_b2996.mif', '-add', 'err_sdm.mif', '-add', '0', 'eroded_mask.mif', '-if', 'safe_mask.mif', '-datatype', 'bit']]
Command: mrcalc err_b5.mif err_b998.mif -add err_b1998.mif -add err_b2996.mif -add err_sdm.mif -add 0 eroded_mask.mif -if safe_mask.mif -datatype bit
mrcalc: [INFO] opening image "err_b5.mif"...
mrcalc: [INFO] image "err_b5.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [INFO] opening image "err_b998.mif"...
mrcalc: [INFO] image "err_b998.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [INFO] opening image "err_b1998.mif"...
mrcalc: [INFO] image "err_b1998.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [INFO] opening image "err_b2996.mif"...
mrcalc: [INFO] image "err_b2996.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [INFO] opening image "err_sdm.mif"...
mrcalc: [INFO] image "err_sdm.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] opening image "eroded_mask.mif"...
mrcalc: [INFO] image "eroded_mask.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [INFO] creating image "safe_mask.mif"...
mrcalc: [INFO] image "safe_mask.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [100%] computing: (((((err_b5.mif + err_b998.mif) + err_b1998.mif) + err_b2996.mif) + err_sdm.mif) ? 0 : eroded_mask.mif)
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrcalc -> mrcalc
dwi2response: [DEBUG] run.version_match() (from run.py:348): Version-matched executable for mrcalc: /home/zzc/mrtrix3/bin/mrcalc
dwi2response: [DEBUG] run._shebang() (from run.py:355): File "/home/zzc/mrtrix3/bin/mrcalc": Not a text file
dwi2response: [DEBUG] run.command() (from dhollander.py:145): To execute: [['/home/zzc/mrtrix3/bin/mrcalc', 'safe_mask.mif', 'full_sdm.mif', '0', '-if', '10', '-min', 'safe_sdm.mif']]
Command: mrcalc safe_mask.mif full_sdm.mif 0 -if 10 -min safe_sdm.mif
mrcalc: [INFO] opening image "safe_mask.mif"...
mrcalc: [INFO] image "safe_mask.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Bit
mrcalc: [INFO] opening image "full_sdm.mif"...
mrcalc: [INFO] image "full_sdm.mif" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [INFO] opening image "0"...
mrcalc: [INFO] opening image "10"...
mrcalc: [INFO] creating image "safe_sdm.mif"...
mrcalc: [INFO] image "safe_sdm.mif" created with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mrcalc: [100%] computing: min ((safe_mask.mif ? full_sdm.mif : 0), 10)
dwi2response: [DEBUG] run.exe_name() (from run.py:561): mrstats -> mrstats
dwi2response: [DEBUG] run.version_match() (from image.py:233): Version-matched executable for mrstats: /home/zzc/mrtrix3/bin/mrstats
dwi2response: [DEBUG] run.exe_name() (from image.py:233): /home/zzc/mrtrix3/bin/mrstats -> /home/zzc/mrtrix3/bin/mrstats
dwi2response: Command: '/home/zzc/mrtrix3/bin/mrstats safe_mask.mif -output mean -output median -output std -output std_rv -output min -output max -output count -mask safe_mask.mif' (piping data to local storage)
dwi2response: [ERROR] Error trying to calculate statistics from image 'safe_mask.mif'
dwi2response: Scratch directory retained; location: /home/zzc/SC_Martix/dwi2response-tmp-NX2EQ2/