[Mristudio-users] How to Process Siemens Mosaic files in DTIStudio?

[Helen Carlson]

Hi all,
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.

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.

The resulting FA and Color maps are of poor resolution. I suspect this is because the wrong b0 is used in the noise calculations.

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.

Thank-you in advance for your help.
Regards,
Helen.

~~~~~~~~




Orginal message:

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: mristudio-users-bounces at mristudio.org<http://lists.mristudio.org/mailman/listinfo/mristudio-users>
[mailto:mristudio-users-bounces at mristudio.org<http://lists.mristudio.org/mailman/listinfo/mristudio-users>] On Behalf Of Anuar Imanbayev
Sent: Thursday, January 15, 2009 2:08 PM
To: mristudio-users at mristudio.org<http://lists.mristudio.org/mailman/listinfo/mristudio-users>
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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