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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>There are two ways to do the reslice. One
is to reslice the raw DWIs or reslice images after tensor calculation. Either
way, you can use the "reslice" function in Landmarker.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>1) Reslice DWIs: Because you want z
reslice, you first have to convert your 1,900 Dicom to a series of 3D volume
data. You can easily do it by DtiStudio. Read all Dicom and save each 3D data
as raw or analyze format (I recommend raw). You have to read each 3D volume to
Landmarker and reslice it to the dimension and pixel size you want. The only
problem of this approach is, you have to repeat it many times. For example, if
you have 2 b0 and 30 DWIs, you have to do it 32 times. Landmarker can read text
script, but it doesn't have butch processing capability. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>2) Reslice after tensor calculation: Here
you have two choices. You can read and reslice tensor elements by Landmarker.
Then you can reload the resliced tensor into DtiStudio to recalculate
eivenvalues, eigenvectors, and other maps like FA. The procedure is;<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>> Calculate tensor by DtiStudio. Save
each element (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) separately as a regular floating
point image or save them into one file (so called *.d file in DtiStudio).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>> Load the image into Landmarker. If
the 6 elements are saved separately, you have to read them individually. If you
save them into one *.d file, you need to use "Open *.d" button to
load all at once.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>(Please obtain the latest Landmarker
because old versions can not interpolate tensor data. Also, the first image you
open is always treated as a template in Landmarker and "Open *.d" is
inactivated. You have to open the image you want to interpolate in the second
window (first image can be anything because we don't use it for this
interpolation operation). First please open a scalar image such as b0 or FA. Then
you can find "Open *.d" in the right column of the window)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>> The interpolation button at in the
bottom of "Image" section, second from the right. Type in the new
dimensions and perform relice.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>> Save the 6 interpolated tensor
elements into one file (new *.d file). Just for the sake of procedure, also
reslice one scalar image such as b0 and save it.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>> Load the resliced scalar image (e.g. b0
with the new dimension) to DtiStudio. You can see "Open *.d" button
in the right column of the viewing window. Load the new interpolated *.d into
DtiStudio. In the dialog window, check "eigenvalues/vectors". <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>The second option is, first calculate all
the scalar maps such as FA and interpolate them. This can be easily done by
Landmarker;<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>> Load a FA map and interpolate using
the button described above.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>These three ways lead to slightly
different results. Visually the tensor interpolation tends to enhance FA
contrast. For example, if there are two adjacent pixels with FA = 0.8 but fiber
angles with 90 degree difference, FA interpolation between these two pixels
gives FA = 0.8, but tensor interpolation gives FA < 0.8. Between two
different fibers with different angles, there remain low FA regions with the
tensor interpolation. I believe the raw DWI interpolation leads to image
similar to the tensor interpolation, but not sure. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>This may give you impression that the
tensor interpolation is the right thing to do. However, if the two adjacent
pixels (FA = 0.8) belong to one continuous fiber with angle transition of 30
degree, you want to keep the same FA (FA = 0.8) between the two pixels. In
this case, you don't want decrease in FA every time you interpolate pixels with
slight angle difference. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>In reality, if you do fiber tracking,
angle transition greater than 40-45 degree is rejected usually. Also, average
angle transition is usually very small (<10), unless 2-2.5 mm image
resolution is too large with respect to fiber curvature. So this may not pose a
large practical issue.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Anyway, as long as we don't know the exact
neuroanatomy of each pixel, there is no single "right interpolation".
You just have to stick with a consistent method. Or you can do both and apply
the same manual ROI or voxel-based method to make sure there is no significant
difference depending on the interpolation (and I doubt there would be). <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hope it helps.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Susumu<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
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face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b><span style='font-weight:
bold'>On Behalf Of </span></b><st1:Street w:st="on"><st1:address w:st="on">Shmuel
Miron Dr</st1:address></st1:Street><br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, June 04, 2008
9:16 AM<br>
<b><span style='font-weight:bold'>To:</span></b> mristudio-users@mristudio.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [Mristudio-users]
reslicing DTI images</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'>Hello List members</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'>I have a large set of DTI data with a
voxel dimension of 1 x 1 x 2.6 mm acquired in the axial position . </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'>However, In DTI studio the resolution on
the sagital and coronal views is not satisfactory.</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'>Is there a way to re-slice the data
(around 1900 dicom images) into voxels of 2.6 x 2.6 x 2.6 mm in DTI
studio ?</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'>Is it possible to perform the job with a
different software? </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'>Thanks</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'> </span></font><o:p></o:p></p>
<div>
<p class=MsoNormal><font size=2 color=purple face="Times New Roman"><span
style='font-size:11.0pt;color:purple'>Dr. Shmuel Miron</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=purple face="Times New Roman"><span
style='font-size:11.0pt;color:purple'>Multiple <st1:place w:st="on"><st1:PlaceName
w:st="on">Sclerosis</st1:PlaceName> <st1:PlaceType w:st="on">Center</st1:PlaceType></st1:place></span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=2 color="#333399" face="Trebuchet MS"><span
style='font-size:10.0pt;font-family:"Trebuchet MS";color:#333399'> </span></font><o:p></o:p></p>
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