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

[Anuar Imanbayev]

Hello Dr. Mori,

I'm very glad to hear from you.

1.) I loaded the data fine. However, in the pull-down menu in the right column of the view window, it only displays [IMA\ - 15] thru [IMA\ - 30] and [IMA\ - 46] to [IMA\ - 52], which are just the raw data images that I've been provided with. There is a catch yet. I've only received parts 2 and 4 of this data set. I'm awaiting parts 1 and 3 and hopefully those will have the b0 and standard images. At the same time, they may be just more raw data files. 

So far I've got:
[IMA\ - 15] to [IMA\ - 30] which comprises part 2
[IMA\ - 46] to [IMA\ - 52] which comprises part 4. 
I'm missing:
[IMA\ - 1] to [IMA\ - 14] which should comprise part 1
[IMA\ - 31] to [IMA\ - 45] which should comprise part 3

2.) I do know of the gradient table. I have contacted the collaborating doctor asking him to provide the gradient table his technicians used for image acquisition. Hopefully, as you've said, the image numbers provide a clue. To me they don't because they just look like raw single-type image files.

3.) My operating system is a Dell Inspiron 9400 32-bit Interl(R) Core(TM) Duo CPU T2350 @1.86GHz 1.87 GHz, so it's up to date. Now, I'm not sure about this imaging plane being oblique. I don't think it is because I can view the images fine and dandy on DTIStudio.

Thank you very much for your time and assistance,
In the meantime, I'll try and circumvent the problem by utilizing MRIConvert to get these .ima mosaic files into .pars and .recs somehow, if possible.

Sincerely yours,
Anuar Imanbayev

----- Original Message -----
From: susumu <susumu at mri.jhu.edu>
Date: Thursday, January 15, 2009 4:00 pm
Subject: Re: [Mristudio-users] How to Process Siemens Mosaic files in	DTIStudio?
To: "'DTI Studio, ROI Editor,	Landmarker Questions/Support'" <mristudio-users at mristudio.org>


> 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
>  [ On Behalf Of Anuar Imanbayev
>  Sent: Thursday, January 15, 2009 2:08 PM
>  To: mristudio-users at mristudio.org
>  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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