Thanks Susumu and Xin, I'll download the air files and try again.<div><br></div><div>Siewmin<br><br><div class="gmail_quote">On Tue, May 12, 2009 at 2:25 AM, susumu <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-US" link="blue" vlink="blue">
<div>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">For those who are interested in image
normalization by Landmarker, here I attached a step-by-step instruction.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">Siewmin, I could transform your data with
the default setup using this procedure.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">Susumu</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy"> </span></font></p>
<div>
<div align="center" style="text-align:center"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">
<hr size="2" width="100%" align="center">
</span></font></div>
<p><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">
<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>
[mailto:<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>] <b><span style="font-weight:bold">On Behalf Of </span></b>Siewmin Gan<br>
<b><span style="font-weight:bold">Sent:</span></b> Monday, May 11, 2009 12:21
PM<div><div></div><div class="h5"><br>
<b><span style="font-weight:bold">To:</span></b> DTI Studio, ROI Editor,
Landmarker Questions/Support<br>
<b><span style="font-weight:bold">Subject:</span></b> Re: [Mristudio-users]
transformations with AIR in Landmarker</div></div></span></font></p>
</div><div><div></div><div class="h5">
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Hi Susumu, I have learnt a lot from your correspondence, as usual. Will
try as you've suggested.</span></font></p>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Thanks</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Siewmin</span></font></p>
<div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<div vlink="blue" link="blue">
<div>
<div align="center" style="text-align:center"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">
<hr size="2" width="100%" align="center">
</span></font></div>
<p style="margin-bottom:12.0pt"><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"> <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>
[<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>]
On Behalf Of susumu [<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>]<br>
<b><span style="font-weight:bold">Sent:</span></b> Sunday, May 10, 2009 9:39 AM<br>
<b><span style="font-weight:bold">To:</span></b> 'DTI Studio, ROI Editor,
Landmarker Questions/Support'<br>
<b><span style="font-weight:bold">Subject:</span></b> Re: [Mristudio-users]
transformations with AIR in Landmarker</span></font></p>
</div>
<div>
<div>
<div>
<div>
<div>
<p><font size="3" color="navy" face="Times New Roman"><span style="font-size:12.0pt;color:navy">Siewmin raised some important points and I hope other users could
gain some important information from this thread.</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> I
got the mean DWI and tensor file from the original 4D DWI. The tensor file is
as you've said, which contains "Dxx, Dyy, Dzz, Dxy, Dxz Dyz" in
one file. In Landmarker, I loaded only the mean DWI of the subject and then the
tensor file with the "open .d" button. The 4D raw DWI is not used in
Landmarker or later. With the "linear" option in AIR, I could rotate
the tensor and the mean DWI to the template DWI without having to subsample the
input data first. The "nonlinear" option requires the subject data
(mean DWI and the tensor file) to be of the same dimension as the template (i.e
181, 217, 181 if ICBM81 DWI is used as template). This is noted in the pop up
message, and it would only continue once the input files are resampled to the
template. </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">>It is always advised to do linear transformation first.
To start non-linear, you have to make sure that the brain locations and shapes
are as similar as possible. This is similar to non-linear fitting. You always
have to provide “initial” values close to the real solutions. Otherwise,
non-linear fitting could converge to a wrong solution (trapped by “local
minima”).</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Additionally,
I tried affine in the linear registration option. The output DWI of the
registration is identical to the input of the DWIs if I used one of my
subject's DWI as the template. Using the 2nd order polynomial in nonlinear
option, an error message occurs "registration terminated due to a calculation
problem, please try a lower order model". It seems to only work if the
template is one of those provided in Landmarker.</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> If you can send us two images you are having the
problem, we can take a look at why AIR doesn’t work.</span></font></p>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">I then
saved the rotated tensor file as one file in the .dat format and the linearly
registered 3D meanDWI. In MRIview3D, I loaded this new 3D DWI and open
this new tensor.dat file with the open.dat button to re-calculates the fa,
colour map etc. I viewed the colour map output from this and it looks pretty
good, and as described previously. </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> This is the correct procedure.</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">I saved
the fa and principal eigenvector file and used them to perform fiber-tracking.
The tracts that are manually extracted obtained looks similiar to the fiber
tracts from the original raw 4D DWI. </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> That is a good sign.</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">The FA
values of these tracts are smaller uniformly in comparison, and the assymetry
preserved (i.e the left tract FA is smaller than the right tract FA using the
maps calculated from the original and rotated tensor). </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> Normalization requires pixel interpolation, which leads
to decreased FA. So you can not compare FA values with and without
normalization.</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">If the
non-linear option is used, is there a problem that the tensor is subsampled
first before it is re-oriented, as described above? </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> As I mentioned above, nonlinear should be AFTER linear
transformation. This means, the data are transformed multiple times and pixels
are interpolated multiple times. To avoid this, once you did linear (save
transformation matrix: T-linear) and nonlinear (save transformation matrix:
T-nonlinear), you can combine the T-linear x T-nonlinear using one of the
buttons in the LDDMM section. Once you combined all transformation matrices,
you can apply it only once to the original image in the native space.</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> Another interesting thing is, there are two ways to
transform images; transform your image to an atlas or transform atlas (usually,
binary segmentation map) to your original data for automated segmentation. For
the latter approach, you don’t have to transform (therefore interpolate) your
original data. When you transform the atlas (segmentation map), make sure to
use “nearest neighbor” (no interpolation), not the tri-linear interpolation.
The segmentation map consists of arbitrary numbers assigned to each segment
(e.g. the internal capsule is “1” and the corona radiata is “3”). If you
interpolate these two segments and obtain “2” in between these two segments and
if “2” means pons, you would get the pons in between the internal capsule and
the corona radiata. On the other hand, when you are transforming your data to
an atlas space, use the tri-linear interpolation. Otherwise, you could get
strange discontinuity artifacts.</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Do you
suggest using the affine or non-linear transformation of the DWIs and the
corresponding transformation of the tensor? Lastly, I'm not sure if the
colour map display is of an issue? It occurs both using the linear affine
option and the non-linear option.</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> When everything is working right, the color map should
look smooth and clean. Maybe you are using “nearest neighbor” for the tensor
transformation?</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Thanks</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Siewmin</span></font></p>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">On Sat,
May 9, 2009 at 7:44 AM, susumu <<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>> wrote:</span></font></p>
<div>
<div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">First, I
tried rotating the tensor but had problems with the results. When I look at the
colour map from the resulting tensor, it looks ok generally, but there are
certain areas of blotchiness and some mixing of colours especially in the
sidelines of white matter regions (i.e there can be a striking red line or a
blotch of redness in the middle of a green regions within the saggital
stratum). These are the steps I took, and would like to check if it is done
correctly.</span></font></p>
</div>
</div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">1.
resample mean DWI of subject data (together with the 4D DTI data and the
tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order trilinear)
the resampled meandwi of subject to dwi of template, and used that to drive the
transformation of the resampled 4D DTI and the resampled tensor simultaneously.
(The resampled tensor was loaded with the .dat button.) I used MRIview 3D to
load the normalised 4D DTI, followed by the normalised tensor with the .dat
button, and calculate the fa, colour etc maps from the normalised tensor. I
tried various thresholding with AIR but the colour maps problem remains.</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> First of all, I think you don't have to resample DTI
images before AIR. AIR can take data with different matrix and pixel sizes and
the output images have the same matrix/pixel dimensions as the template (in
your case, 181x217x181 of ICBM81).</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> By saying "4D DTI", do you mean raw 4D DWI
before tensor calculation? if so, I don't think you want transform raw DWIs. If
you want to do anything to raw DTI, you also want to transform the
corresponding gradient table, which could be messy. Our tools do not provide methods
to transform raw DWIs.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> When you say, "tensor" data, I assume you are
talking about 4D file that contains "Dxx, Dyy, Dzz, Dxy, Dxz, Dyz"
images in one file. If so, please make sure that you load this 4D tensor file
by the "open .d" button in Landmarker. Once read in Landmarker, the
4D tensor file is disassembled to 6 3D data for Dxx, Dyy, Dzz, Dxy, Dxz, Dyz.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> Once the AIR is done using mean DWI (your data) - mean
DWI (template), the 6 3D tensor element data should be stored all together into
one file as a "transformed 4D tensor file".</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> This transformed 4D tensor file needs to be read into
DtiStudio to re-calculate new transformed FA, color, vec, etc.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> The blotch-looking colormap could happen by; 1)
transform the color map directly (you should recreate color maps using the
recalcuated FA and vector files from the transformed tensor file or 2) you
transformed a vector file (transformed vector files should be obtained from the
transformed tensor file. Vector can not be directly transformed).</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Second, I
tried without rotating the tensor. I calculate the scalar and colour maps from
the original 4D DTI data, aligned the maps to AC-PC line, draw rois on them and
invert transform the rois back to native dti space to extract the relevant
white matter tracts. I had two problems here. 1) with orienting the
subjects scalar DWI to another particular subject's DWI with rigid
transformation in AIR and 2) Invert transform ROIs drawn on the registered
colour map back to the original DTI space. These are the steps I took:</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> Maybe you are transforming raw DWI data? Again, you
should not transform raw DWI and recalcuate tensor. You have to first calculate
tensor (throw away the raw DWIs) and transform the tensor.</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">1. A
subject's data which is acquired // to AC-PC is chosen and other subjects not
acquired //to AC are registered to this. Again the meanDWI is used for source
and target images, this time using rigid transformation in AIR in Landmarker.
However, there is no difference detected after the transformation has taken
place. However, if I change the target image from a subject's DWI to the mean
DWI of the ICBM 81 template, it works but the source data would be subsampled
to that of the ICBM template. I'm not sure why it didn't work in the 1st
case? </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> As mentioned above, AIR not only adjust the image
orientation and translation, but also the matrix / pixel size..</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> Rigid transformation of AIR is sometimes very cranky. We
are working on alternative methods now. please try different threshold or
affine.</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Additionally,
using either another subject or the template DWI as target image, would yield
the an output file (AlignlinearOutput.air) when the transformation has been
performed, which I saved the invert_AlignlinearOutput.air. However, when I
clicked on these .air files in the folder it is saved as an installer package,
I get the following error message " An error has occurred.The
application could not be installed because the AIR file is damaged. Try
obtaining a new AIR file from the application author." I have installed
the air application and placed it in the same folder, together with the
alignlinear.exe file. Is it possible to view the transformation matrix files
saved or did I not installed the air application appropriately?</span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> Maybe Xin can answer this question better, but I'm not
sure why you want to open *.air??</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> Once you save the *.air, you can load it back to
Landmarker and apply to images by using the "open M" button in the
LDDMM section.</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">2. ROIs
are drawn on the transformed AC-PC aligned colour maps with
ROI-editor. I would like to check if it's OK to draw rois on the
transformed colour map? These ROIs would later be used as the start ROI
and stop ROI to extract the corresponding white matter tract with DTI
studio) </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> Drawing ROIs on color maps is fine. ROI is simply 1/0
information about which pixels you chose and the color maps are simply what is
displayed to aid your ROI drawing. </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> If you draw ROI in the atlas space and have a plan to
back-transform your ROI files to the native space, there are several things you
have to know;</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">1) Atlas space is 1x1x1 and your native space could be 2-3
mm. The ROI defined in the thin 1 mm slice could be lost after transformation
to the thick 2-3mm slice. Therefore, you have to create 3D ROIs in the atlas
space with at least 3mm thick</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">2) Use nearest neighbor interpolation when you back-transfer.
You don't want to get a pixel with 0.3 or 0.4 after transformation. You want
1/0</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">3. I
tried to invert-transform these ROIs back to the original DTI space with
the previously saved invert_matrix.air file. How is that done in Landmarker and
if the previous error message needs to be resolved before I can used the matrix
files? </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<p><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">> Xin, how to do the invert-transformation of *.air?</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" color="navy" face="Times New Roman"><span style="font-size:12.0pt;color:navy">Susumu</span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
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