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<div dir="ltr"><font face="Tahoma" color="#000000" size="2">Hi Susumu,</font></div>
<div dir="ltr"><font face="tahoma" size="2">Thank you very much for all your help.</font></div>
<div dir="ltr"><font face="tahoma" size="2"></font> </div>
<div dir="ltr"><font face="tahoma" size="2">Since we do use oblique angles I am currently exploring option 5-1 below. My question is:
</font><font face="Tahoma" size="2">Is there a way I can manually determine which file is which for putting them in six different directories? Is there something in the header that would allow me to write a script to do this automatically? At the moment there
does not seem to be a logical naming sequence that I can use to seperate them out.</font></div>
<div dir="ltr"><font face="tahoma" size="2"></font> </div>
<div dir="ltr"><font face="tahoma" size="2">Thank-you again.</font></div>
<div dir="ltr"><font face="tahoma" size="2">Helen.</font></div>
<div dir="ltr"><font face="tahoma" size="2"></font> </div>
<div dir="ltr"><font face="Tahoma" size="2"></font> </div>
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<div><font color="#000080"><font size="1"><font face="Tahoma"><strong>Helen Carlson</strong>, Ph.D.</font></font></font></div>
<div><font face="tahoma" color="#000080" size="1">Neuropsychology</font></div>
<div><font face="tahoma" color="#000080" size="1">Department of Neurosciences</font></div>
<div><font face="tahoma" color="#000080" size="1">Alberta Children's Hospital</font></div>
<div><font face="tahoma" color="#000080">
<div><font face="Tahoma" color="#000080" size="1"></font> </div>
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<font face="Tahoma" size="2"><b>From:</b> mristudio-users-bounces@mristudio.org [mristudio-users-bounces@mristudio.org] On Behalf Of susumu mori [susumu@mri.jhu.edu]<br>
<b>Sent:</b> July 22, 2009 8:01 PM<br>
<b>To:</b> DTI Studio, ROI Editor, Landmarker Questions/Support<br>
<b>Subject:</b> Re: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio?<br>
</font><br>
</div>
<div></div>
<div>Hi Helen,<br>
<br>
1) You have 42 mosaic files. This means, you did (1 b0 + 6 DWI) x 6 repetitions, I think.<br>
2) In recent Siemens system, if you do signal averaging, the scanners save the repeated measurements separately instead of averaging them. This enables you to do image co-registration to minimize motion-related problems. Please note that if the scanners average
multiple acquisitions, you can not do co-registration anymore. <br>
3) There are two ways to load the 42 images; a) load all of them as one sequential data, b) load the data as 6 independent (1 b0 + 6 DWI) data.<br>
4) You loaded the data as #a method. In this case, you have to modify your b-table. For example, if your b-table is;<br>
<br>
0: 0, 0, 0<br>
1: 1, 1, 0<br>
2: 1, 0, 1<br>
3: 0, 1, 1<br>
4: -1, 1, 0<br>
5: -1,0, 1<br>
6: 0, -1,1<br>
<br>
you have to repeat this 6 times like;<br>
<br>
0: 0, 0, 0<br>
1: 1, 1, 0<br>
2: 1, 0, 1<br>
3: 0, 1, 1<br>
4: -1, 1, 0<br>
5: -1,0, 1<br>
6: 0, -1,1<br>
7: 0, 0, 0<br>
8: 1, 1, 0<br>
9: 1, 0, 1<br>
10: 0, 1, 1<br>
11: -1, 1, 0<br>
12: -1,0, 1<br>
13: 0, -1,1<br>
.<br>
.<br>
and so on.<br>
<br>
5) Method #a should work fine, but Method #b has several advantages. For example, you can calculate standard deviations and subtraction images for the 6 repeated measurements. These repeated measurements should look identical. You can easily see if the subject
moves and if co-registration works fine. Corrupted images can be detected much easiler too. There are two ways to convert the 42 sequential data to 6 repeated parallel data;<br>
5-1) Separate the 42 IMA files into 6 different directories (1 b0 + 6 DWIs in each directory) and list the 6 directories in the DtiStudio data input window. This can be most easily done if you can specify the scanner to save the data in this way (I thought
it's possible). Otherwise, you may find it difficult to figure out how to divide the 42 files into the 6 repeated data.<br>
5-2) Once you read the 42 IMA data, you can save them as 6 raw files; each raw file contains 7 images. You can do it by using the "save" icon in the right column. Close the window and load the raw data as the "REC" format. Load the all 6 raw files at once.
One problem is, during the conversion of Mosaic -> Raw, you loose information about oblique imaging (see #6), which means you should not use this method if you used oblique angles.<br>
<br>
In both cases, the b-table will be;<br>
<br>
0: 0, 0, 0<br>
1: 1, 1, 0<br>
2: 1, 0, 1<br>
3: 0, 1, 1<br>
4: -1, 1, 0<br>
5: -1,0, 1<br>
6: 0, -1,1<br>
<br>
6) As I mentioned multiple times in the previous communications, Siemens users have to be very careful when oblique imaging is used. Unless you are using the latest VB15 operating system, the gradient table has to be recalculated based on the oblique angles.
This can be done by checking the box ("rotate if applicable") beneath the b-table window. DtiStudio automatically reads the angle information from Dicom/Mosaic headers and rotate the b-table. If you are using VB15, this is already taken care of at the time
of data acquisition and therefore you don't check this box. If you convert the Dicom/Mosaic to a raw data format (REC format), the oblique information is lost and you can not use this function. Therefore the approach #5-2 can not be used unless you are not
using oblique imaging.<br>
<br>
Susumu<br>
<br>
<div class="gmail_quote">On Wed, Jul 22, 2009 at 4:40 PM, Helen Carlson <span dir="ltr">
<<a href="mailto:Helen.Carlson@albertahealthservices.ca">Helen.Carlson@albertahealthservices.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<div>
<div dir="ltr"><font face="Tahoma" color="#000000" size="2">Hi all,</font></div>
<div dir="ltr"><font face="tahoma" size="2">I am trying to create a tensor image from a 6 direction DTI scan and am having trouble. I can load my 42 IMA images successfully into DTI Studio (they are in mosaic format). However I would expect to see 7 options
in the drop down list on the right side of the Image tab. These options should be composed of a b0 and the 6 DWI directions.</font></div>
<div dir="ltr"><font face="tahoma" size="2"></font> </div>
<div dir="ltr"><font face="tahoma" size="2">However, I see 42 options in the drop down list. As I scroll through these options I see 7 b0 images interleaved with 6 diffusion weighted images between them giving me the 42 images in the list.</font></div>
<div dir="ltr"><font face="tahoma" size="2"></font> </div>
<div dir="ltr"><font face="tahoma" size="2">The resulting FA and Color maps are of poor resolution. I suspect this is because the wrong b0 is used in the noise calculations.</font></div>
<div dir="ltr"><font face="tahoma" size="2"></font> </div>
<div dir="ltr"><font face="tahoma" size="2">So my question is, what am I doing wrong while loading the data that causes this? I searched the archives and found an email (below) addressing this issue. It was helpful though I still cannot resolve my problem.</font></div>
<div dir="ltr"><font face="tahoma" size="2"></font> </div>
<div dir="ltr"><font face="tahoma" size="2">Thank-you in advance for your help.</font></div>
<div dir="ltr"><font face="tahoma" size="2">Regards,</font></div>
<div dir="ltr"><font face="tahoma" size="2">Helen.</font></div>
<div dir="ltr"> </div>
<div dir="ltr">~~~~~~~~</div>
<div><font face="Tahoma" size="1"></font> </div>
<div><font face="tahoma" color="#000080">
<div><font face="Tahoma" color="#000080" size="1"></font> </div>
<div><font face="tahoma" size="1"></font> </div>
<div>
<pre>Orginal message:</pre>
<pre>Hi Anuar,
1) Could you read the IMA (mosaic format data)? If so, make sure how many
images are loaded. You can use "MRIView3D -> Siemens Mosaic" and load the
data. If successful, you should see a list of loaded images in the pull-down
menu in the right column of the viewing window. For example, if you used
typical Siemens 12-orientation scheme, you should find 1 b0 + 12 DWI (total
13 images).
2) Then you need to find a correct gradient table. If you are using an
off-the-shelf Siemens DTI method, there are Siemens-supplied gradient tables
for that. If you don't know the table, please let us know, together with the
number of images you get in the step #1. If you are using a user-specified
table, you need to find the table.
3) Final thing you have to check is the version of your operating system and
oblique plane angle. If you are using the latest operating system or your
imaging plane is not oblique, you are fine. If you are using an old
operating system AND an oblique plane, than, you have to check "Rotate
gradients if applicable" box.
Susumu
-----Original Message-----
From: <a href="http://lists.mristudio.org/mailman/listinfo/mristudio-users" target="_blank">mristudio-users-bounces at mristudio.org</a>
[mailto:<a href="http://lists.mristudio.org/mailman/listinfo/mristudio-users" target="_blank">mristudio-users-bounces at mristudio.org</a>] On Behalf Of Anuar Imanbayev
Sent: Thursday, January 15, 2009 2:08 PM
To: <a href="http://lists.mristudio.org/mailman/listinfo/mristudio-users" target="_blank">mristudio-users at mristudio.org</a>
Subject: [Mristudio-users] How to Process Siemens Mosaic files in DTIStudio?
Hello everyone,
I usually deal with .par and .rec files. However, my PI's collaborator works
with Siemens Mosaic files and needs help in being able to perform tensor
calculations on them. I'm working out the kinks so then I can report
sometime next week with my findings.
At first, the collaborating doctor informed me that the files were .IMA
files. Indeed they did masquerade as those, but in reality responded only to
Siemens Mosaic filetype under DTIStudio.
Dr. Hangyi Jiang identified the data files not as ima but as mosaic files
for me and helped me around in general. Still, I'm at a loss with which
gradient files to treat these Siemens Mosaic files and how to perform Tensor
calculations that produce credible color maps (mine so far were just red
dots all around) I'll keep experimenting and poking around in the meantime.
Please help me understand and deal with this new file type. Also, apparently
there were no b0 or standard data files associated with the data set that
the collaborator sent - just a bunch of image files. Would that be a
problem in the long run? How to handle the situation when those are
provided? With just image files, how do I go about creating an image quality
file, then saving it after my scanning for bad quality images?
Thank you for your time and assistance in advance,
Sincerely yours,
Anuar Imanbayev
Undergraduate Neuroscience 2010
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