Import the main analysis module and tractography module. Use the analysis module to download a raw brain of interest, then use the tractography function "nii_to_tiff_stack" to save a .nii as a TIFF stack.
In [1]:
import tractography as tract
In [2]:
import analysis3 as a3
In [3]:
output = a3.get_raw_brain("s275", "userToken.pem", resolution = 5, save = True)
In [4]:
tract.nii_to_tiff_stack("s275_raw.nii", "s275")
In [5]:
data = tract.tiff_stack_to_array("s275_TIFFs/")
(62, 51, 1114)
In [6]:
output = tract.generate_FSL_structure_tensor(data, "s275")
Start DoG Sigma on 1
Start Gauss Sigma with gausigma = 2.3
Generating Gaussian kernel...
Blurring gradient products...
Saving a copy for this Gaussian sigma...
Completed computing structure tensor on s275!
In [7]:
print output
[[[[ 1.17211079e-03 4.61393298e-04 4.29590815e-04 1.18349027e-03
5.82360779e-04 8.46458040e-03]
[ 1.75740977e-03 6.87447435e-04 3.98420147e-04 1.77207997e-03
6.44385349e-04 1.14451321e-02]
[ 2.41538463e-03 9.29222791e-04 3.85111751e-04 2.43816711e-03
7.03715777e-04 1.44598400e-02]
...,
[ 1.82602147e-03 9.09190916e-04 -8.17735199e-05 2.15542666e-03
-1.46867416e-04 8.35172273e-03]
[ 1.50017091e-03 6.78559416e-04 1.57159142e-04 1.68193295e-03
1.27213498e-04 7.03569176e-03]
[ 1.20673736e-03 4.98128415e-04 2.78341293e-04 1.29545608e-03
2.64797331e-04 5.34076942e-03]]
[[ 1.59076368e-03 4.97569446e-04 5.80972875e-04 1.13690377e-03
5.56790386e-04 1.14370435e-02]
[ 2.38564098e-03 7.43634766e-04 5.29687211e-04 1.70573976e-03
5.93669771e-04 1.54217118e-02]
[ 3.27508710e-03 1.00224023e-03 5.01179951e-04 2.34626536e-03
6.26834633e-04 1.94152426e-02]
...,
[ 2.66696839e-03 1.07043260e-03 -2.19439753e-04 2.17685313e-03
-2.76094564e-04 1.13392416e-02]
[ 2.14943266e-03 7.77045672e-04 1.46880309e-04 1.66850537e-03
5.17653352e-05 9.48769785e-03]
[ 1.69827708e-03 5.52878482e-04 3.42366082e-04 1.26388262e-03
2.25922806e-04 7.16846902e-03]]
[[ 1.98619091e-03 5.13362000e-04 7.32669316e-04 9.53714247e-04
4.33694513e-04 1.41119901e-02]
[ 2.97997100e-03 7.71552383e-04 6.57445809e-04 1.43730245e-03
4.15195769e-04 1.89450514e-02]
[ 4.08488512e-03 1.03432755e-03 6.04293833e-04 1.97526417e-03
3.91252339e-04 2.37172097e-02]
...,
[ 3.65355005e-03 1.21816690e-03 -4.70814295e-04 1.96808041e-03
-4.49481013e-04 1.39549319e-02]
[ 2.87985313e-03 8.57576262e-04 5.81731802e-05 1.47234718e-03
-8.36622057e-05 1.15873218e-02]
[ 2.22480507e-03 5.85491769e-04 3.56018805e-04 1.08654622e-03
1.25232618e-04 8.71116668e-03]]
...,
[[ 1.79413974e-03 -4.83728916e-04 5.86165290e-04 2.01979768e-03
-9.82319820e-04 1.17381057e-02]
[ 2.66172434e-03 -7.07844039e-04 5.35911822e-04 2.98819761e-03
-1.18201657e-03 1.57815963e-02]
[ 3.56088299e-03 -9.42064100e-04 4.84556687e-04 3.99167836e-03
-1.29942317e-03 1.97742023e-02]
...,
[ 2.02978379e-03 -5.77120169e-04 3.66298918e-04 2.30757613e-03
-3.04810703e-04 1.25280973e-02]
[ 1.86059065e-03 -5.31456491e-04 4.53417510e-04 2.11987947e-03
-3.73611314e-04 1.04762819e-02]
[ 1.58020249e-03 -4.55021422e-04 4.80086775e-04 1.80413551e-03
-3.98027216e-04 7.81580899e-03]]
[[ 1.45450188e-03 -5.48732118e-04 4.44111065e-04 2.36803782e-03
-1.03694014e-03 9.01136827e-03]
[ 2.15807045e-03 -8.03532312e-04 3.96837248e-04 3.49868648e-03
-1.22488150e-03 1.20721580e-02]
[ 2.87444610e-03 -1.06587540e-03 3.44663917e-04 4.66931472e-03
-1.32233428e-03 1.50480699e-02]
...,
[ 1.53262552e-03 -6.17204001e-04 2.79353670e-04 2.70265224e-03
-3.30087525e-04 9.44064464e-03]
[ 1.40454969e-03 -5.70566743e-04 3.43359716e-04 2.48831115e-03
-4.02797916e-04 7.89733138e-03]
[ 1.19252468e-03 -4.89212573e-04 3.62364488e-04 2.11945013e-03
-4.28230007e-04 5.89279924e-03]]
[[ 1.05412223e-03 -5.24413073e-04 3.02914617e-04 2.34216661e-03
-9.28034424e-04 6.20846311e-03]
[ 1.56439433e-03 -7.68630300e-04 2.64685834e-04 3.45744588e-03
-1.07695698e-03 8.28974973e-03]
[ 2.07595062e-03 -1.01692276e-03 2.20139496e-04 4.61020553e-03
-1.14137749e-03 1.02829728e-02]
...,
[ 1.03833899e-03 -5.58186439e-04 1.91071158e-04 2.65755458e-03
-3.01560853e-04 6.38179341e-03]
[ 9.51263763e-04 -5.17285429e-04 2.33308761e-04 2.45029526e-03
-3.67105822e-04 5.34019805e-03]
[ 8.07402015e-04 -4.43979312e-04 2.45444855e-04 2.08829949e-03
-3.89657187e-04 3.98539100e-03]]]
[[[ 1.21579098e-03 5.59776730e-04 3.97050637e-04 1.67342031e-03
8.21766211e-04 1.18099703e-02]
[ 1.82897958e-03 8.33147729e-04 2.96158629e-04 2.50500115e-03
8.90002120e-04 1.58788059e-02]
[ 2.50368449e-03 1.11083663e-03 2.01154340e-04 3.43514932e-03
9.39165126e-04 1.98997296e-02]
...,
[ 1.95535319e-03 1.14872854e-03 -2.05190416e-04 3.05685494e-03
-2.87367293e-04 1.13275042e-02]
[ 1.55240949e-03 8.27859330e-04 7.93832369e-05 2.36545294e-03
1.19794575e-04 9.49692167e-03]
[ 1.21151027e-03 5.83146291e-04 2.38476874e-04 1.80603482e-03
3.33196571e-04 7.18074897e-03]]
[[ 1.66547450e-03 6.17951737e-04 5.45337680e-04 1.61601417e-03
7.93294574e-04 1.59810744e-02]
[ 2.50612479e-03 9.23479965e-04 3.96713935e-04 2.42387224e-03
8.23122973e-04 2.14196388e-02]
[ 3.42619116e-03 1.22992788e-03 2.53772741e-04 3.32342880e-03
8.31629499e-04 2.67381724e-02]
...,
[ 2.97312788e-03 1.47728820e-03 -4.57128685e-04 3.19296867e-03
-5.29276615e-04 1.53459748e-02]
[ 2.31198710e-03 1.04057975e-03 -3.27309886e-06 2.42348341e-03
-2.35159368e-05 1.27754528e-02]
[ 1.76405883e-03 7.09856278e-04 2.63348629e-04 1.81338424e-03
2.58775690e-04 9.61630512e-03]]
[[ 2.10608752e-03 6.57945522e-04 7.13396352e-04 1.36713975e-03
6.41074381e-04 1.97422709e-02]
[ 3.16909980e-03 9.88855492e-04 5.15940948e-04 2.05853442e-03
5.95486141e-04 2.63318717e-02]
[ 4.32445481e-03 1.31405483e-03 3.16935650e-04 2.82037607e-03
5.26400516e-04 3.26708928e-02]
...,
[ 4.29750979e-03 1.88534590e-03 -9.05943860e-04 3.06891440e-03
-8.70149001e-04 1.88707076e-02]
[ 3.26887099e-03 1.30518072e-03 -2.23137351e-04 2.27437122e-03
-2.78360472e-04 1.55868446e-02]
[ 2.42881943e-03 8.62102199e-04 1.99813818e-04 1.65185507e-03
7.89176920e-05 1.16797853e-02]]
...,
[[ 1.80540432e-03 -4.56666632e-04 5.52637037e-04 2.79508834e-03
-1.34131697e-03 1.60952620e-02]
[ 2.68383115e-03 -6.68073946e-04 4.63780307e-04 4.13554907e-03
-1.59836793e-03 2.15749238e-02]
[ 3.57957114e-03 -8.92082287e-04 3.68372217e-04 5.51622687e-03
-1.73503289e-03 2.69182008e-02]
...,
[ 1.90846832e-03 -5.51096164e-04 3.83051229e-04 3.11886868e-03
-4.14758309e-04 1.68330651e-02]
[ 1.74204051e-03 -5.11573220e-04 4.77742578e-04 2.86644045e-03
-5.11483231e-04 1.40925059e-02]
[ 1.47732801e-03 -4.42475546e-04 5.01978153e-04 2.44216761e-03
-5.44842682e-04 1.05306888e-02]]
[[ 1.47124380e-03 -5.15877735e-04 4.22529847e-04 3.26828216e-03
-1.41508109e-03 1.23307826e-02]
[ 2.18745810e-03 -7.55070010e-04 3.53339012e-04 4.82894806e-03
-1.65854162e-03 1.64735354e-02]
[ 2.90487497e-03 -1.00456586e-03 2.75928294e-04 6.43551815e-03
-1.77081814e-03 2.04530619e-02]
...,
[ 1.44230144e-03 -5.86485083e-04 2.92064273e-04 3.64437024e-03
-4.48835723e-04 1.26676261e-02]
[ 1.31540454e-03 -5.47034782e-04 3.61157174e-04 3.35694477e-03
-5.50807919e-04 1.06113367e-02]
[ 1.11459463e-03 -4.73964232e-04 3.77891993e-04 2.86247511e-03
-5.85247413e-04 7.93200918e-03]]
[[ 1.07253075e-03 -4.94195265e-04 2.91102449e-04 3.22698127e-03
-1.26681686e-03 8.48261826e-03]
[ 1.59517955e-03 -7.24070123e-04 2.42448412e-04 4.76363394e-03
-1.46039459e-03 1.12973927e-02]
[ 2.11058580e-03 -9.60439153e-04 1.85588709e-04 6.34311931e-03
-1.53203483e-03 1.39616244e-02]
...,
[ 9.78328637e-04 -5.28583245e-04 1.99922637e-04 3.57690151e-03
-4.10392327e-04 8.55167862e-03]
[ 8.91393865e-04 -4.94626176e-04 2.45196366e-04 3.29993106e-03
-5.02162613e-04 7.16734165e-03]
[ 7.54660752e-04 -4.29137785e-04 2.55481573e-04 2.81574228e-03
-5.32414531e-04 5.35938470e-03]]]
[[[ 1.14688266e-03 6.54040079e-04 3.14064033e-04 2.18740432e-03
1.08683703e-03 1.52014606e-02]
[ 1.73337385e-03 9.72127600e-04 1.20411598e-04 3.27086402e-03
1.14799326e-03 2.02858150e-02]
[ 2.35758303e-03 1.27584243e-03 -9.25100903e-05 4.46315389e-03
1.15602976e-03 2.51417700e-02]
...,
[ 2.02460797e-03 1.46558252e-03 -4.20285418e-04 4.11839038e-03
-5.47812961e-04 1.40134636e-02]
[ 1.51983253e-03 1.01550715e-03 -8.09383273e-05 3.14561045e-03
3.19671381e-05 1.16702206e-02]
[ 1.12275360e-03 6.79892837e-04 1.29609747e-04 2.36626226e-03
3.53125040e-04 8.77834391e-03]]
[[ 1.59167137e-03 7.42402102e-04 4.56266687e-04 2.12827791e-03
1.07203866e-03 2.05919426e-02]
[ 2.40478432e-03 1.10783021e-03 1.82556352e-04 3.18727992e-03
1.08012231e-03 2.73812637e-02]
[ 3.26602068e-03 1.45584054e-03 -1.21290119e-04 4.34834883e-03
1.02986058e-03 3.37906182e-02]
...,
[ 3.26771708e-03 2.08353740e-03 -8.63690220e-04 4.50227549e-03
-9.82258120e-04 1.89715382e-02]
[ 2.41232337e-03 1.43051671e-03 -3.00591113e-04 3.37283337e-03
-2.33435087e-04 1.56844147e-02]
[ 1.73982698e-03 9.37251956e-04 6.51419250e-05 2.47885659e-03
2.09706326e-04 1.17513919e-02]]
[[ 2.05299305e-03 8.19299952e-04 6.59561192e-04 1.82521285e-03
9.25006927e-04 2.54552029e-02]
[ 3.09559074e-03 1.22624729e-03 3.11488489e-04 2.73875403e-03
8.41037312e-04 3.36640328e-02]
[ 4.19253111e-03 1.61212741e-03 -8.69466821e-05 3.73163121e-03
6.94765244e-04 4.12775688e-02]
...,
[ 5.05130785e-03 2.93911109e-03 -1.63089309e-03 4.64710966e-03
-1.60871423e-03 2.33988296e-02]
[ 3.67622846e-03 2.01944076e-03 -7.55167275e-04 3.41101200e-03
-6.94345043e-04 1.91952419e-02]
[ 2.58903089e-03 1.30623183e-03 -1.57390125e-04 2.43169046e-03
-1.08668275e-04 1.43373813e-02]]
...,
[[ 1.58021599e-03 -3.55214957e-04 4.38874791e-04 3.48846591e-03
-1.64244126e-03 2.01305896e-02]
[ 2.35608290e-03 -5.20808157e-04 3.11659620e-04 5.16215945e-03
-1.92455971e-03 2.69016474e-02]
[ 3.13003897e-03 -7.01585261e-04 1.68406463e-04 6.88049104e-03
-2.05010665e-03 3.34152877e-02]
...,
[ 1.51737418e-03 -4.33736132e-04 3.64296313e-04 3.84313497e-03
-5.21535112e-04 2.05736142e-02]
[ 1.37614063e-03 -4.10192675e-04 4.58229624e-04 3.53596522e-03
-6.47469831e-04 1.72555298e-02]
[ 1.16487558e-03 -3.62557475e-04 4.74349654e-04 3.01833916e-03
-6.88393717e-04 1.29263308e-02]]
[[ 1.28996838e-03 -3.90391244e-04 3.38482612e-04 4.06431826e-03
-1.72970560e-03 1.53498519e-02]
[ 1.92395574e-03 -5.72202611e-04 2.52948405e-04 6.00607786e-03
-2.00171117e-03 2.04551611e-02]
[ 2.54588854e-03 -7.68331171e-04 1.54932961e-04 7.99939968e-03
-2.10619182e-03 2.53033601e-02]
...,
[ 1.14748580e-03 -4.55451809e-04 2.75167113e-04 4.47330810e-03
-5.61700494e-04 1.54493833e-02]
[ 1.03806052e-03 -4.33327543e-04 3.42896063e-04 4.12511779e-03
-6.93923561e-04 1.29683968e-02]
[ 8.76753300e-04 -3.83826933e-04 3.53338575e-04 3.52416211e-03
-7.35837151e-04 9.71980393e-03]]
[[ 9.44512081e-04 -3.71536938e-04 2.36387845e-04 4.00286261e-03
-1.54849235e-03 1.05199106e-02]
[ 1.40930584e-03 -5.44955663e-04 1.84505421e-04 5.90993837e-03
-1.76755548e-03 1.39815891e-02]
[ 1.85849727e-03 -7.29169813e-04 1.23121034e-04 7.86538608e-03
-1.83245912e-03 1.72264930e-02]
...,
[ 7.80176080e-04 -4.07186686e-04 1.87392274e-04 4.37745359e-03
-5.13196515e-04 1.04075009e-02]
[ 7.03929749e-04 -3.89174354e-04 2.31285885e-04 4.04369598e-03
-6.31840376e-04 8.74323491e-03]
[ 5.93188510e-04 -3.45391833e-04 2.37110449e-04 3.45726451e-03
-6.68230699e-04 6.55654352e-03]]]
...,
[[[ 3.06933955e-03 -1.39211235e-03 -1.39423937e-03 5.20391017e-03
2.38897395e-03 1.32095739e-02]
[ 4.79847705e-03 -2.06914637e-03 -1.60993286e-03 8.31494387e-03
2.50232825e-03 1.74279343e-02]
[ 6.70164078e-03 -2.73037772e-03 -1.63572154e-03 1.17288344e-02
2.19140621e-03 2.12844592e-02]
...,
[ 2.70990911e-03 -1.34582072e-03 -4.06007021e-04 4.74574743e-03
3.13611701e-04 1.10899946e-02]
[ 2.47035222e-03 -1.14530802e-03 -4.41621727e-04 4.03905613e-03
4.44411213e-04 9.63501446e-03]
[ 2.07969546e-03 -8.99098697e-04 -4.16044932e-04 3.15399957e-03
4.96920373e-04 7.47149484e-03]]
[[ 6.05012430e-03 -2.47583096e-03 -2.75622169e-03 9.59140714e-03
4.78242384e-03 2.07485054e-02]
[ 9.65303555e-03 -3.62402364e-03 -3.28525109e-03 1.54372612e-02
5.10468846e-03 2.74195280e-02]
[ 1.36366654e-02 -4.69984394e-03 -3.36498814e-03 2.18515061e-02
4.40910412e-03 3.33810858e-02]
...,
[ 4.78227297e-03 -2.34015146e-03 -3.81844147e-04 8.46415013e-03
-1.17640877e-04 1.52673172e-02]
[ 4.23648441e-03 -1.99374114e-03 -3.46050627e-04 7.10616168e-03
-1.60250238e-05 1.34041701e-02]
[ 3.45783168e-03 -1.55602721e-03 -2.77070008e-04 5.41004492e-03
6.42503801e-05 1.05577121e-02]]
[[ 1.17327599e-02 -4.35235677e-03 -5.22946985e-03 1.69833545e-02
9.25287511e-03 3.22310142e-02]
[ 1.89518239e-02 -6.22243527e-03 -6.38293521e-03 2.72039995e-02
1.00413579e-02 4.29424234e-02]
[ 2.69407015e-02 -7.88385607e-03 -6.57991553e-03 3.83437164e-02
8.69931281e-03 5.24941571e-02]
...,
[ 8.73624906e-03 -4.39357758e-03 4.98644768e-05 1.58394836e-02
-1.19030429e-03 1.98736638e-02]
[ 7.55854137e-03 -3.81602743e-03 3.15592246e-04 1.33040324e-02
-1.28445181e-03 1.79387461e-02]
[ 5.99519024e-03 -3.02293757e-03 4.81202762e-04 1.00515997e-02
-1.21727388e-03 1.46311736e-02]]
...,
[[ 2.52318323e-01 2.37117544e-01 -1.97751135e-01 2.95507550e-01
-2.60908782e-01 8.83216083e-01]
[ 3.78749371e-01 3.51561874e-01 -2.22627535e-01 4.33862329e-01
-2.93119460e-01 1.12663198e+00]
[ 5.10118783e-01 4.68844086e-01 -2.17080906e-01 5.73427200e-01
-2.78593838e-01 1.31364453e+00]
...,
[ 2.31216848e-01 1.97848067e-01 8.14420208e-02 2.78899461e-01
1.00103974e-01 5.94003439e-01]
[ 1.80016115e-01 1.68374792e-01 6.61084503e-02 2.40480974e-01
8.27394873e-02 4.42644715e-01]
[ 1.32841393e-01 1.35547385e-01 4.50493619e-02 1.95377216e-01
5.85838147e-02 2.91345686e-01]]
[[ 1.51124150e-01 1.60862371e-01 -1.21135585e-01 2.25479499e-01
-1.72432110e-01 5.10531127e-01]
[ 2.28489548e-01 2.40814969e-01 -1.37592703e-01 3.35415840e-01
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In [ ]:
Content source: NeuroDataDesign/seelviz
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