[Insight-users] MR-SPECT REgistration using Rigid Transform
CSPL
hyd2_affable at sancharnet.in
Wed, 7 Apr 2004 12:13:23 +0530
This is a multi-part message in MIME format.
------=_NextPart_000_000D_01C41C99.B91DD2D0
Content-Type: text/plain;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Hi All,
I have been working in Registration of MRI and SPECT Images of same =
patient Brain.
MR dimensions are 256 X 256 X 120 and 0.859382 \ 0.859375 \ 1.60000.
My moving image is SPECT image.Actual dimensions are 128 X 128 X 47 with =
voxel dimensions 1.802125\1.802125\3.60425.
SPECT image undergoes a ForceCubic operation and Its dimensions changes =
to 128X 128 X 95 and voxel dimesnions to 1.802125 \ 1.802125 \ 1.802125.
And it is in Transverse View.=20
As MR image is in Coronal view i changed the Spect to coronal before =
giving it to the Registration. So,After changing its view to coronal its =
dimensions become=20
128 X 95 X 128 and 1.802125 \ 1.802125 \ 1.802125.SPECT with these =
dimensions is given to the registration process.
I used the following itk classes:
MattesMutualInformationImageToImageMetric,RecursiveMultiResolutionPyramid=
ImageFilter,
QuaternionRigidTransform,RegularStepGradientDescentOptimizer,RecursiveMul=
tiResolutionPyramidImageFilter.
And the input parameters are :
Translate scale value is 1/10000, iterations are 150, scales =3D 1, max =
step length =3D 4.0, min step length =3D 0.005, bins =3D 35, samples =3D =
1000, levels =3D 3.
I added observer to the process and i am getting the following values :
First Level:
0 -0.320374 [0.0100438, -0.0350144, 0.0105636, 0.986362, =
-0.553508, -0.00411211, 0.831858]
1 -0.321063 [0.030953, -0.0382486, -0.00937501, 0.999558, =
-0.00125347, -0.440459, 1.5415]
2 -0.371695 [0.0659527, -0.0315038, -0.0302047, 0.974523, =
0.0133357, -1.43741, 1.60113]
3 -0.389297 [0.0748733, -0.0149963, -0.0518501, 0.992978, =
0.962366, -1.64413, 1.8366]
4 -0.473205 [0.0765801, -0.0308507, -0.0461271, 1.0002, 0.831316, =
-1.52403, 2.30357]
5 -0.489634 [0.0867224, -0.0318137, -0.0522786, 1.01073, 1.15721, =
-1.6065, 2.67335]
-------------------------------
20 -0.526699 [0.0869593, -0.0339316, -0.0559707, 1.01556, 1.18742, =
-1.66461, 2.72034]
21 -0.526875 [0.086819, -0.0340573, -0.056085, 1.01558, 1.19139, =
-1.65994, 2.72518]
22 -0.527021 [0.0867698, -0.0341474, -0.0562826, 1.0156, 1.19699, =
-1.65843, 2.73041]
23 -0.527126 [0.0866777, -0.0342297, -0.0564333, 1.01563, =
1.20222, -1.65538, 2.73534]
-----------------------------------------------
47 -0.528611 [0.0852474, -0.0356566, -0.058518, 1.015, 1.25176, =
-1.57546, 2.82544]
48 -0.528646 [0.0852217, -0.0356863, -0.0585624, 1.015, 1.25251, =
-1.57258, 2.82797]
49 -0.528681 [0.0852033, -0.0357116, -0.0586277, 1.01498, =
1.25373, -1.57004, 2.83068]
---------------------------------------------
144 -0.525427 [0.0845718, -0.0363607, -0.0603638, 1.01422, =
1.22735, -1.23997, 2.96168]
145 -0.525436 [0.0845504, -0.0363369, -0.06038, 1.01423, 1.22755, =
-1.2361, 2.96218]
146 -0.52494 [0.0845361, -0.0363315, -0.0603705, 1.01426, =
1.22752, -1.23235, 2.96328]
147 -0.52495 [0.0847016, -0.036275, -0.0605773, 1.01413, 1.22964, =
-1.23218, 2.96654]
148 -0.525374 [0.0846794, -0.0363122, -0.0605381, 1.01414, =
1.22845, -1.23069, 2.96692]
149 -0.525412 [0.0846573, -0.036348, -0.0605014, 1.01415, =
1.22734, -1.22913, 2.96732]
Second Level:
0 -0.418512 [0.0887451, -0.0189369, -0.077675, 1.00696, 2.20275, =
-1.37414, 3.13128]
1 -0.418945 [0.0836208, -0.0236872, -0.0630348, 1.01192, 2.22691, =
-0.917966, 3.33384]
2 -0.413912 [0.0652313, -0.0161832, -0.0486405, 1.00361, 2.10126, =
-0.505873, 3.08141]
3 -0.371655 [0.0629191, -0.00723327, -0.0532294, 1.01451, =
2.54857, -0.291537, 3.14261]
4 -0.361762 [0.0715741, -0.0131997, -0.059176, 1.02901, 2.72654, =
-0.369328, 3.60296]
5 -0.367962 [0.0714853, -0.0257059, -0.0513781, 1.02656, 2.41281, =
-0.219652, 3.96205]
6 -0.388251 [0.0817307, -0.0310034, -0.0601911, 1.01481, 2.18368, =
-0.662284, 3.99708]
7 -0.41388 [0.0881204, -0.03356, -0.0638268, 0.991765, 1.87106, =
-1.04525, 3.92623]
----------------------------
53 -0.444609 [0.0904033, -0.0317655, -0.0649183, 0.986647, =
2.28652, -1.12252, 4.21855]
54 -0.444668 [0.0903786, -0.0317895, -0.0648504, 0.986712, =
2.29139, -1.12121, 4.22452]
55 -0.444666 [0.0904111, -0.0317457, -0.064888, 0.986666, =
2.29744, -1.12326, 4.22902]
56 -0.44467 [0.0903941, -0.0317951, -0.0648093, 0.986712, 2.3017, =
-1.12212, 4.23546]
57 -0.44468 [0.0904166, -0.0317319, -0.064856, 0.986649, 2.30811, =
-1.12411, 4.23945]
58 -0.444699 [0.0903994, -0.0317871, -0.0647737, 0.986687, =
2.31225, -1.12307, 4.24599]
----------------------------------
146 -0.445491 [0.0900287, -0.0319401, -0.0639129, 0.985568, =
2.73939, -1.19044, 4.6637]
147 -0.445511 [0.0900287, -0.031949, -0.0639108, 0.985541, =
2.74461, -1.19175, 4.66937]
148 -0.445525 [0.0900161, -0.0319461, -0.0639007, 0.985548, =
2.75007, -1.19225, 4.67494]
149 -0.445532 [0.090016, -0.0319676, -0.0638845, 0.985523, =
2.75507, -1.19321, 4.68086]
Third Level:
0 -0.302895 [0.112791, -0.0365895, -0.0844165, 1.00896, 3.33379, =
-1.60939, 5.38112]
1 -0.322343 [0.0992007, -0.0304807, -0.0782828, 1.00517, 3.25472, =
-1.32882, 4.97522]
2 -0.313556 [0.101683, -0.0331957, -0.0747196, 1.01122, 3.1463, =
-1.1917, 5.15378]
3 -0.328914 [0.0990012, -0.0300732, -0.0743876, 1.0092, 3.13413, =
-1.19278, 5.02946]
4 -0.330295 [0.0997371, -0.0316464, -0.0740325, 1.00807, 3.0786, =
-1.21719, 5.0444]
5 -0.332905 [0.100176, -0.0317067, -0.0743968, 1.00936, 3.0995, =
-1.2133, 5.06726]
---------------------------
35 -0.338694 [0.100619, -0.031991, -0.0749333, 1.01022, 3.03826, =
-1.2607, 5.02906]
36 -0.33863 [0.100617, -0.0320048, -0.0749167, 1.01019, 3.03661, =
-1.26134, 5.02824]
37 -0.338678 [0.100626, -0.0320129, -0.0749159, 1.01021, 3.03511, =
-1.26227, 5.02739]
38 -0.338677 [0.10062, -0.0319927, -0.0749215, 1.01021, 3.03419, =
-1.26311, 5.02589]
-------------------------
59 -0.338709 [0.100639, -0.0320017, -0.0748891, 1.01031, 3.00697, =
-1.27972, 5.00324]
60 -0.338664 [0.100631, -0.0319735, -0.0749054, 1.01029, 3.00644, =
-1.28063, 5.0016]
61 -0.338709 [0.100639, -0.0320041, -0.0748886, 1.01031, 3.00458, =
-1.28112, 5.00129]
62 -0.338667 [0.10063, -0.0319716, -0.074908, 1.0103, 3.00421, =
-1.28205, 4.9996]
63 -0.33871 [0.100645, -0.0320181, -0.074882, 1.01033, 3.00229, =
-1.28225, 4.99989]
First and Second Levels took all the 150 iterations and at third levels =
process came out at 65th iteration. I tried to change the tranlate scale =
value to less than 1000. Becuase for mr volumes 100 is sufficient.But, I =
am gettign the itk errorr message "All the sampled points are moved =
outof the image regios.
Please anybody explain me the better way to achieve good registration =
output.
Regards,
Srivalli.
------=_NextPart_000_000D_01C41C99.B91DD2D0
Content-Type: text/html;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.2600.0" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV> </DIV>
<DIV><FONT face=3DArial size=3D2>Hi All,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2> I have been working in =
Registration of MRI=20
and SPECT Images of same patient Brain.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>MR dimensions are 256 X 256 X 120 =
and=20
0.859382 \ 0.859375 \ 1.60000.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>
<DIV><FONT face=3DArial size=3D2>My moving image is SPECT image.Actual =
dimensions=20
are 128 X 128 X 47 with voxel dimensions =
1.802125\1.802125\3.60425.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>SPECT image undergoes a ForceCubic =
operation and=20
Its dimensions changes to 128X 128 X 95 and voxel dimesnions to 1.802125 =
\=20
1.802125 \ 1.802125.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>And it is in Transverse View. =
</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>As MR image is in Coronal view i =
changed the Spect=20
to coronal before giving it to the Registration. So,After changing its =
view to=20
coronal its dimensions become <BR></FONT><FONT face=3DArial =
size=3D2>128=20
X 95 X 128 and 1.802125 \ 1.802125 \ 1.802125.SPECT =
with these=20
dimensions is given to the registration process.</FONT></DIV>
<DIV></FONT><FONT face=3DArial size=3D2></FONT> </DIV></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I used the following itk =
classes:</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>MattesMutualInformationImageToImageMetric,RecursiveMultiResoluti=
onPyramidImageFilter,</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>QuaternionRigidTransform,RegularStepGradientDescentOptimizer,Rec=
ursiveMultiResolutionPyramidImageFilter.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>And the input parameters are =
:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Translate scale value is 1/10000, =
iterations are=20
150, scales =3D 1, max step length =3D 4.0, min step length =3D 0.005, =
bins =3D 35,=20
samples =3D 1000, levels =3D 3.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I added observer to the process and i =
am getting=20
the following values :</FONT></DIV>
<DIV><FONT face=3DArial size=3D4><STRONG>First =
Level:</STRONG></FONT></DIV>
<DIV><FONT face=3DArial size=3D2> 0 =
-0.320374 =20
[0.0100438, -0.0350144, 0.0105636, 0.986362, -0.553508, =
-0.00411211,=20
0.831858]<BR> 1 -0.321063 =
[0.030953,=20
-0.0382486, -0.00937501, 0.999558, -0.00125347, -0.440459,=20
1.5415]<BR> 2 -0.371695 =
[0.0659527,=20
-0.0315038, -0.0302047, 0.974523, 0.0133357, -1.43741,=20
1.60113]<BR> 3 -0.389297 =
[0.0748733,=20
-0.0149963, -0.0518501, 0.992978, 0.962366, -1.64413,=20
1.8366]<BR> 4 -0.473205 =
[0.0765801,=20
-0.0308507, -0.0461271, 1.0002, 0.831316, -1.52403,=20
2.30357]<BR> 5 -0.489634 =
[0.0867224,=20
-0.0318137, -0.0522786, 1.01073, 1.15721, -1.6065, =
2.67335]<BR></FONT><FONT=20
face=3DArial size=3D2>-------------------------------</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>20 =
-0.526699 =20
[0.0869593, -0.0339316, -0.0559707, 1.01556, 1.18742, -1.66461,=20
2.72034]<BR> 21 -0.526875 =
[0.086819,=20
-0.0340573, -0.056085, 1.01558, 1.19139, -1.65994,=20
2.72518]<BR> 22 -0.527021 =
[0.0867698,=20
-0.0341474, -0.0562826, 1.0156, 1.19699, -1.65843,=20
2.73041]<BR> 23 -0.527126 =
[0.0866777,=20
-0.0342297, -0.0564333, 1.01563, 1.20222, -1.65538, =
2.73534]<BR></FONT><FONT=20
face=3DArial =
size=3D2>-----------------------------------------------</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>47 =
-0.528611 =20
[0.0852474, -0.0356566, -0.058518, 1.015, 1.25176, -1.57546,=20
2.82544]<BR> 48 -0.528646 =
[0.0852217,=20
-0.0356863, -0.0585624, 1.015, 1.25251, -1.57258,=20
2.82797]<BR> 49 -0.528681 =
[0.0852033,=20
-0.0357116, -0.0586277, 1.01498, 1.25373, -1.57004, =
2.83068]</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>---------------------------------------------</FONT></DIV>
<DIV><FONT face=3DArial size=3D2> 144 =20
-0.525427 [0.0845718, -0.0363607, -0.0603638, =
1.01422,=20
1.22735, -1.23997, 2.96168]<BR> 145 =
-0.525436 =20
[0.0845504, -0.0363369, -0.06038, 1.01423, 1.22755, -1.2361,=20
2.96218]<BR> 146 -0.52494 =
[0.0845361,=20
-0.0363315, -0.0603705, 1.01426, 1.22752, -1.23235,=20
2.96328]<BR> 147 -0.52495 =
[0.0847016,=20
-0.036275, -0.0605773, 1.01413, 1.22964, -1.23218,=20
2.96654]<BR> 148 -0.525374 =
[0.0846794,=20
-0.0363122, -0.0605381, 1.01414, 1.22845, -1.23069,=20
2.96692]<BR> 149 -0.525412 =
[0.0846573,=20
-0.036348, -0.0605014, 1.01415, 1.22734, -1.22913, 2.96732]</FONT></DIV>
<DIV><FONT face=3DArial size=3D4><STRONG>Second =
Level:</STRONG></FONT></DIV>
<DIV><FONT face=3DArial size=3D2>0 =
-0.418512 =20
[0.0887451, -0.0189369, -0.077675, 1.00696, 2.20275, -1.37414,=20
3.13128]<BR> 1 -0.418945 =
[0.0836208,=20
-0.0236872, -0.0630348, 1.01192, 2.22691, -0.917966,=20
3.33384]<BR> 2 -0.413912 =
[0.0652313,=20
-0.0161832, -0.0486405, 1.00361, 2.10126, -0.505873,=20
3.08141]<BR> 3 -0.371655 =
[0.0629191,=20
-0.00723327, -0.0532294, 1.01451, 2.54857, -0.291537,=20
3.14261]<BR> 4 -0.361762 =
[0.0715741,=20
-0.0131997, -0.059176, 1.02901, 2.72654, -0.369328,=20
3.60296]<BR> 5 -0.367962 =
[0.0714853,=20
-0.0257059, -0.0513781, 1.02656, 2.41281, -0.219652,=20
3.96205]<BR> 6 -0.388251 =
[0.0817307,=20
-0.0310034, -0.0601911, 1.01481, 2.18368, -0.662284,=20
3.99708]<BR> 7 -0.41388 =
[0.0881204,=20
-0.03356, -0.0638268, 0.991765, 1.87106, -1.04525, 3.92623]</FONT></DIV>
<DIV><FONT face=3DArial =
size=3D2>----------------------------</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>53 =
-0.444609 =20
[0.0904033, -0.0317655, -0.0649183, 0.986647, 2.28652, -1.12252,=20
4.21855]<BR> 54 -0.444668 =
[0.0903786,=20
-0.0317895, -0.0648504, 0.986712, 2.29139, -1.12121,=20
4.22452]<BR> 55 -0.444666 =
[0.0904111,=20
-0.0317457, -0.064888, 0.986666, 2.29744, -1.12326,=20
4.22902]<BR> 56 -0.44467 =
[0.0903941,=20
-0.0317951, -0.0648093, 0.986712, 2.3017, -1.12212,=20
4.23546]<BR> 57 -0.44468 =
[0.0904166,=20
-0.0317319, -0.064856, 0.986649, 2.30811, -1.12411,=20
4.23945]<BR> 58 -0.444699 =
[0.0903994,=20
-0.0317871, -0.0647737, 0.986687, 2.31225, -1.12307, =
4.24599]</FONT></DIV>
<DIV><FONT face=3DArial =
size=3D2>----------------------------------</FONT></DIV>
<DIV><FONT face=3DArial size=3D2> 146 =
-0.445491 =20
[0.0900287, -0.0319401, -0.0639129, 0.985568, 2.73939, -1.19044,=20
4.6637]<BR> 147 -0.445511 =
[0.0900287,=20
-0.031949, -0.0639108, 0.985541, 2.74461, -1.19175,=20
4.66937]<BR> 148 -0.445525 =
[0.0900161,=20
-0.0319461, -0.0639007, 0.985548, 2.75007, -1.19225,=20
4.67494]<BR> 149 -0.445532 =
[0.090016,=20
-0.0319676, -0.0638845, 0.985523, 2.75507, -1.19321, =
4.68086]</FONT></DIV>
<DIV><FONT face=3DArial size=3D4><STRONG>Third =
Level:</STRONG></FONT></DIV>
<DIV><FONT face=3DArial size=3D2>0 =
-0.302895 =20
[0.112791, -0.0365895, -0.0844165, 1.00896, 3.33379, -1.60939,=20
5.38112]<BR> 1 -0.322343 =
[0.0992007,=20
-0.0304807, -0.0782828, 1.00517, 3.25472, -1.32882,=20
4.97522]<BR> 2 -0.313556 =
[0.101683,=20
-0.0331957, -0.0747196, 1.01122, 3.1463, -1.1917,=20
5.15378]<BR> 3 -0.328914 =
[0.0990012,=20
-0.0300732, -0.0743876, 1.0092, 3.13413, -1.19278,=20
5.02946]<BR> 4 -0.330295 =
[0.0997371,=20
-0.0316464, -0.0740325, 1.00807, 3.0786, -1.21719,=20
5.0444]<BR> 5 -0.332905 =
[0.100176,=20
-0.0317067, -0.0743968, 1.00936, 3.0995, -1.2133, 5.06726]</FONT></DIV>
<DIV><FONT face=3DArial =
size=3D2>---------------------------</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>35 =
-0.338694 =20
[0.100619, -0.031991, -0.0749333, 1.01022, 3.03826, -1.2607,=20
5.02906]<BR> 36 -0.33863 =
[0.100617,=20
-0.0320048, -0.0749167, 1.01019, 3.03661, -1.26134,=20
5.02824]<BR> 37 -0.338678 =
[0.100626,=20
-0.0320129, -0.0749159, 1.01021, 3.03511, -1.26227,=20
5.02739]<BR> 38 -0.338677 =
[0.10062,=20
-0.0319927, -0.0749215, 1.01021, 3.03419, -1.26311, =
5.02589]</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>-------------------------</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>59 =
-0.338709 =20
[0.100639, -0.0320017, -0.0748891, 1.01031, 3.00697, -1.27972,=20
5.00324]<BR> 60 -0.338664 =
[0.100631,=20
-0.0319735, -0.0749054, 1.01029, 3.00644, -1.28063,=20
5.0016]<BR> 61 -0.338709 =
[0.100639,=20
-0.0320041, -0.0748886, 1.01031, 3.00458, -1.28112,=20
5.00129]<BR> 62 -0.338667 =
[0.10063,=20
-0.0319716, -0.074908, 1.0103, 3.00421, -1.28205,=20
4.9996]<BR> 63 -0.33871 =
[0.100645,=20
-0.0320181, -0.074882, 1.01033, 3.00229, -1.28225, 4.99989]</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>First and Second Levels took all the =
150 iterations=20
and at third levels process came out at 65th iteration. I tried to =
change the=20
tranlate scale value to less than 1000. Becuase for mr volumes 100 is=20
sufficient.But, I am gettign the itk errorr message "All the sampled =
points are=20
moved outof the image regios.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Please anybody explain me the better =
way to achieve=20
good registration output.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Regards,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Srivalli.</FONT></DIV></BODY></HTML>
------=_NextPart_000_000D_01C41C99.B91DD2D0--