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

[Anuar Imanbayev]

Correction
2.) I do NOT know what gradient table to use at this time.

----- Original Message -----
From: Anuar Imanbayev <aimanba1 at jhu.edu>
Date: Monday, January 19, 2009 5:04 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>


> 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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