how to upload Philips dicom file or ASCII MRSI

[Ping-Hong Yeh]

Hi jMRUI community,

I have Philips 2D CSI PRESS dicom files which i have tried to upload them to the jMRUI, but not successfully. First of all, i was not able to tell water reference files from MRSI files. Does anyone know if there is a dicom tag that can tell them apart. Anyhow, jMRUI was not happy with the dicom format and was not able to read any of them.

I then read the dicom files using matlab scripts and saved the complex FID in ASCII text file in the size of [1024 32 10], where 1024 is sampling points there are 320 dicom files and the VOI is 16×10 (both water reference and CSI files so it makes up 32×10), something like

-149.3+253.76i -239.22+451.15i -259.61+608.01i -171.13+695.71i -79.986+757.23i -104.21+803.34i -297.52+815.18i -452.57+689.53i -510.11+501.89i -392.61+267.38i 5.368+0.36374i 3.5867+0.59017i 7.2588-0.35574i 29.355+2.4995i 31.761+9.2547i 5.4431+3.5224i 17.008+2.3282i 26.815-2.6444i 15.327+1.2498i 19.504+10.875i -131.41+210.33i -231.49+391.15i -265.91+549.25i -213.27+652.31i -134.89+720.84i -161.92+754.93i -328.86+749.42i -469.63+653.4i -485.16+469.07i -372.51+247.8i 4.516+0.76699i 3.9648+1.4755i 6.2942+2.2005i 23.65+5.9162i 26.976+10.747i 7.4328+4.2516i 15.17+5.4953i 17.24-2.289i 10.671-2.4899i 19.404+7.9891i -93.189+155.35i -179.78+317.04i -227.67+489.6i -216.16+628.86i -195.38+720.22i -239.75+738.44i -348.72+682.93i -410.84+562.86i -405.02+407.16i -296.91+215.7i 2.0052+0.19107i 1.7771+1.0202i 5.219+2.67i 14.604+6.5539i 20.731+8.9032i 11.53+4.2808i 15.457+8.0415i 7.788+0.041598i -2.1575-3.1195i 14.399+4.5283i -42.945+98.392i -95.799+229.99i -136.88+390.42i -155.24+548.5i -182.81+657.88i -226.91+682.16i -303.02+609.17i -311.53+479.39i -265.69+313.09i -184.27+163.1i 1.8136+0.47715i 0.82361-0.13487i 2.9559-0.097286i 6.4221+1.7669i 12.115+4.1186i 0.83249+0.67926i -1.1229+3.5765i 6.3+1.4512i 9.1716+5.067i 20.638+10.436i -3.5567+54.344i -19.649+133.71i -43.927+241.94i -72.135+364.97i -121.59+459.8i -154.55+495.61i -190.89+438.16i -177.71+325.98i -140+202.11i -83.219+96.492i 1.4126+1.029i 0.15035-0.45351i 2.7236-0.47388i 8.1651+2.4387i 10.379+3.4538i 3.3304+0.21164i 14.995+7.3507i 33.725+13.981i 30.545+15.473i 19.379+12.718i 18.736+28.595i 18.005+52.878i 10.522+103.21i -16.894+164.25i -40.11+213.4i -56.864+236.33i -71.525+215.35i -59.26+159.68i -45.62+92.677i -28.554+48.804i 0.57413+0.71021i -1.2175-1.704i 0.51109+0.72408i 6.4248+5.0272i 7.7486+5.1637i 9.2135+7.2436i 24.12+19.678i 29.397+23.254i 17.209+14.21i 5.4393+8.2094i 16.191+15.875i 23.405+17.054i 29.072+24.267i 21.645+41.379i 17.495+61.545i 8.177+69.436i 6.4408+66.506i 2.528+59.843i -6.1365+38.755i -9.3635+18.81i 0.51111-0.17467i 0.15148-0.87769i 0.50393-0.67993i 0.51679+1.6363i 0.41575+1.9179i 0.080495+2.6216i 0.99121+5.8463i 1.2212+4.6096i -0.38453+0.90078i -0.60322+1.782i 6.6782+9.3229i 12.534+7.57i 25.333+4.7925i 34.28+6.0597i 36.597+7.7609i 31.549+6.7973i 24.101+7.8365i 10.675+16.116i 0.12445+15.58i -4.3043+9.9745i 0.37597-0.28848i -0.26499-0.026491i 0.041547-0.10383i 0.43007-0.43844i 0.080194-0.024843i -0.82002-0.13269i -0.1399-1.5476i -0.080647-0.90424i -0.11912-0.71906i -0.473-0.18202i 0.068128+0.29797i 2.7416+2.8566i 15.642+8.923i 10.064+0.24687i 3.918+9.2915i 2.644+37.199i 3.7544+64.767i -7.9795+67.517i -3.5156+20.3i 0.064875+0.11843i -0.012105-0.02646i 0.02547-0.14481i -0.013886+0.14737i -0.95133-0.78105i -1.254+0.56811i -0.78226+0.79235i -1.0607+0.98971i -1.8408-0.22841i -0.44979-1.0759i -0.0068686-0.013509i 3.6331+6.4165i 2.3104+35.548i -28.929+45.645i -69.95+62.639i -103.01+89.399i -108.19+105.81i -80.13+113.41i -55.24+91.743i -35.043+71.094i -8.0214+31.621i -0.17973-0.10919i 0.020596+2.4754i 2.4077+1.1377i 2.7415+0.01963i 2.3549+1.6929i 2.8276+2.7631i 1.8098+3.5242i -0.72422+2.9657i -2.2407-1.3861i -0.97374-1.7058i -0.42355+39.793i -39.953+65.955i -130.56+128.12i -228.81+202.19i -297.45+257.24i -314.9+267.38i -257.41+224.35i -170.74+165.14i -78.272+87.241i -17.121+50.239i 7.889+11.476i 21.381+9.6842i 20.063+2.6071i 11.588-0.8771i 10.202+0.32492i 12.682+3.1808i 15.685+5.786i 22.902+9.6052i 12.497+8.2195i -0.072255+1.1978i -26.645+61.275i -123.75+126.98i -247.41+234.64i -386.63+368.1i -493.77+466.5i -518.88+469.8i -447.67+382.74i -317.58+252.85i -164.19+129.63i -50.161+47.672i 22.56+14.483i 31.351+6.6002i 20.561+1.7251i 12.251-1.6064i 9.09-2.7631i 8.0399-2.6074i 22.525+3.8701i 51.652+15.778i 51.128+19.088i 8.7329+6.9877i -73.445+106.63i -207.05+212.73i -341.47+355.78i -452.35+505.8i -537.29+617.26i -569.93+634.96i -534.86+539.51i -434.14+361.59i -276.83+183.84i -122.17+69.473i 24.4+10.133i 21.878+6.7889i 7.8126+3.0165i 11.713-0.23905i 13.826-2.3357i 1.4516-7.6664i 9.1205-0.95309i 33.107+15.43i 63.924+23.069i 33.638+14.251i -135.78+178.55i -254.77+322.2i -356.17+475.56i -392.77+612.42i -417.53+708.77i -446.14+731.74i -478.3+655.21i -464.46+473.55i -369.29+285.26i -224.54+139.3i 18.894+4.3358i 15.609+3.2097i 8.341+2.6172i 22.094+6.2344i 25.572+5.8665i 4.5782-5.9552i 16.96+0.76966i 21.51+11.396i 37.494+19.701i 39.604+15.695i -161.96+243.63i -258.54+421.2i -305.63+591.29i -270.7+697.74i -217.36+770.39i -245.15+798.32i -358.4+760.67i -456.85+610.11i -445.69+411.44i -305.48+213.54i 15.924+1.3569i 9.4993+0.45264i 6.5783+0.22376i 21.931+7.1712i 25.351+10.258i 4.2572-3.6883i 26.367+5.6047i 35.427+9.501i 17.788+9.0529i 27.964+9.336i -160.21+275.48i -248.02+468.34i -267.25+637.32i -176.24+728.11i -90.348+787.69i -115.64+834.53i -283.86+814.72i -450.09+697.71i -489.76+494.29i -362.93+263.56i 11.21-0.39357i 6.8981+0.040886i 8.0974-0.91518i 24.98+3.73i 27.102+10.589i 4.4121+0.58667i 20.608+1.1599i 33.567+1.151i 13.274+5.0007i 23.108+12.181i
-244.81+476.1i -408.17+840.92i -449.32+1128.1i -290.91+1285.4i -125.26+1395.8i -171.31+1480.6i -536.16+1503.6i -829.3+1271.7i -939.36+925.63i -724.91+492.53i 6.0662-6.524i 6.3799-2.2834i 14.716-1.1574i 51.934+4.7292i 55.465+16.714i 11.146+7.3962i 31.141+5.1927i 42.671-13.265i 22.752-17.611i 31.837-19.073i -217+393.54i -402.5+727.03i -469.94+1016.9i -374.87+1204.6i -230.1+1329.4i -279.05+1392.1i -598.47+1381.6i -861.97+1204.2i -894.04+864.09i -687.15+456.48i 4.8111-4.4671i 6.1715-1.1443i 14.356+0.88463i 44.481+10.229i 47.036+16.566i 13.166+5.962i 31.203+11.641i 28.946-2.6816i 14.114-11.588i 33.353-11.458i -152.01+287.97i -313.3+585.79i -406.23+906.33i -385.53+1162.4i -343.64+1330i -422.47+1364i -634.89+1262.6i -752.35+1040.5i -744.17+753.21i -545.91+399.97i 1.925-2.9259i 3.8892+0.86922i 12.007+0.42592i 28.839+11.125i 37.457+16.812i 19.489+5.3671i 28.986+13.197i 12.968-1.5415i -8.3874-6.6126i 21.87+0.37351i -66.136+178.41i -165.25+423.44i -243.16+720.8i -275.92+1013.2i -322.53+1216.3i -401.15+1262.2i -549.08+1129.5i -567.29+888.41i -485.05+581.28i -336.4+304.13i 2.4559-2.6385i 1.1313+0.71314i 5.3299-2.8925i 13.505+0.65355i 21.203+7.4679i -1.1661-0.85966i -3.5774+4.9563i 9.9935-0.014609i 15.993+6.3902i 36.167+14.063i 0.14293+97.208i -30.702+243.82i -77.051+444.86i -126.78+673.56i -214.07+851.14i -273.19+919i -343.89+813.94i -321.31+604.97i -252.9+375.73i -151.37+179.75i 2.3427-0.74649i -0.94183+0.26687i 3.8109-0.47925i 15.684+2.6586i 19.817+5.531i 4.8078-0.55694i 25.873+11.124i 62.398+22.266i 56.829+23.204i 36.235+16.611i 37.172+49.496i 34.22+94.547i 20.304+188.31i -28.184+302.39i -68.992+395.46i -99.478+439.45i -127.59+400.46i -105.62+295.79i -82.02+172.16i -51.452+90.974i 1.3485-0.16854i -3.1318-0.39441i 0.65893+3.1785i 11.888+9.3199i 15.371+9.4384i 18.211+13.623i 45.738+37.033i 56.12+44.415i 32.357+24.968i 11.568+11.568i 30.563+26.902i 43.178+29.197i 53.474+42.629i 40.903+75.049i 33.97+113.75i 16.231+129.37i 12.128+123.2i 6.37+109.51i -10.6+71.623i -16.954+35.191i 0.11318-0.8596i -1.0153-0.87106i -0.094162-1.2067i 0.59742+2.5288i 1.0047+3.5675i 1.0631+5.4972i 1.6287+11.698i 0.99034+10.355i -1.5011+3.4593i 0.093901+2.2845i 13.131+15.92i 23.526+12.654i 46.808+7.1859i 63.508+9.7745i 67.718+13.735i 57.603+12.305i 43.391+13.423i 19.675+29.253i 0.57888+28.649i -7.8117+18.582i -0.053557-0.91024i -0.66236+0.1399i -0.036011-0.23604i 1.023-0.99436i 0.65645+0.065518i -1.4008+0.52522i -1.1086-2.5932i -0.70422-1.632i -0.86914-0.90039i -0.8367-0.20409i 0.17877+0.52066i 6.1653+5.1672i 38.713+17.593i 26.813+2.6043i 10.966+18.621i 4.6633+68.745i 8.1202+117.7i -13.598+123.11i -6.2788+37.24i 0.12786+0.23821i -0.044354-0.021535i -0.25691-0.3326i 0.592-1.0314i -1.8193-0.3185i -2.6035+1.2548i -0.43798+2.0916i 0.72702+2.4745i -2.4238+2.8479i -1.5776-0.057684i -0.020185-0.0096368i 9.7524+11.788i 22.368+69.116i -34.158+89.917i -114.13+121.6i -182.85+168.01i -198.51+194.78i -146.24+206.06i -99.948+168.26i -63.103+132.9i -14.012+60.433i -0.28357-0.064571i 1.4848+2.9508i 3.2693-1.8014i 2.305-4.9003i 4.5689-1.9316i 6.4814-0.74537i 5.9618+1.049i 2.285+3.5448i -3.5154+0.62941i -3.3397-0.32222i 20.076+77.541i -46.283+129.76i -211.96+248.23i -402.08+382.86i -540.17+478.72i -578.79+492.15i -472.52+410.93i -311.41+305.58i -142.25+165.69i -30.526+94.167i 22.363+4.3231i 35.823-13.376i 24.003-22.98i 9.9833-17.808i 10.407-14.862i 16.736-16.825i 22.431-17.966i 33.166-22.912i 23.07-10.506i 1.6928+0.88756i -23.483+119.46i -193.93+247.43i -424.89+448.79i -692.82+692.45i -901.7+867.1i -952.86+867.51i -820.59+707.12i -579.59+472.74i -299.6+244.3i -91.585+91.47i 43.862-10.167i 41.963-32.97i 23.538-26.16i 12.592-16.406i 7.413-13.596i 6.4725-21.39i 30.55-29.412i 69.722-53.947i 73.644-52.95i 17.287-6.3244i -107.16+205.41i -345.92+409.59i -597.61+676.76i -812.96+949.86i -978.45+1148.4i -1041+1176.4i -974.46+1002.4i -789.95+680.64i -505.7+349.61i -224.36+134.8i 38.536-20.439i 31.826-20.466i 14.307-5.8666i 20.486+0.50163i 17.111-4.5942i -8.45-23.088i 12.618-16.576i 51.936-24.41i 88.571-65.349i 50.21-33.253i -218.14+341.26i -431.77+613.29i -621.1+899.45i -697.23+1147.3i -749.58+1318.2i -803.92+1357.5i -862.46+1220.1i -843.91+888.47i -673.92+540.45i -412.68+265.8i 24.269-20.073i 20.646-15.643i 15.771+0.52626i 41.209+15.067i 41.111+12.947i -3.3586-18.669i 23.252-15.655i 43.085+5.7706i 63.47-23.497i 58.096-39.503i -263.68+461.31i -435.15+793.88i -522.54+1109.2i -465.89+1300.6i -373.57+1428i -427.47+1478i -637.39+1413.4i -829.08+1138.3i -814.46+771.92i -562.41+401.12i 17.093-20.926i 11.588-11.461i 11.664+1.2962i 39.325+14.434i 44.021+21.011i 0.38609-5.113i 39.972-7.0309i 62.089-2.0869i 33.891-5.5409i 38.713-29.391i -260.2+518.02i -416.88+876.8i -453.9+1187.6i -292.73+1349.4i -139.52+1454.5i -188.81+1540.4i -502.54+1507.9i -819.9+1293.2i -898.76+917.7i -669.44+489.1i 10.177-16.231i 9.2053-7.8028i 14.38-1.2585i 43.853+8.9503i 50.633+22.253i 8.4729+3.8632i 32.176-1.7397i 53.027-16.837i 21.624-15.62i 34.902-25.256i

JMRUI is still not happy with ASCII format, any suggestions?

Thanks.

Ping

Ping-Hong Yeh
Uniformed Services University of the Health Sciences

[Jacob Ross]

Hi Everyone,

I am having a similar problem to Ping-Hong Yeh. I exported spectra from TopSpin in the ASCII format, but jMRUI has trouble uploading these files.

Thanks for your help!

Jacob Ross

Henry Ford Health System

• This reply was modified 6 years ago by Jacob Ross.
• This reply was modified 6 years ago by Jacob Ross.
• This reply was modified 6 years ago by Jacob Ross.

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