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

Wed Jul 22 22:01:24 EDT 2009

Hi Helen,

1) You have 42 mosaic files. This means, you did (1 b0 + 6 DWI) x 6
repetitions, I think.
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.
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.
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;

0: 0, 0, 0
1: 1, 1, 0
2: 1, 0, 1
3: 0, 1, 1
4: -1, 1, 0
5: -1,0, 1
6: 0, -1,1

you have to repeat this 6 times like;

0: 0, 0, 0
1: 1, 1, 0
2: 1, 0, 1
3: 0, 1, 1
4: -1, 1, 0
5: -1,0, 1
6: 0, -1,1
7: 0, 0, 0
8: 1, 1, 0
9: 1, 0, 1
10: 0, 1, 1
11: -1, 1, 0
12: -1,0, 1
13: 0, -1,1
.
.
 and so on.

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;
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.
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.

In both cases, the b-table will be;

0: 0, 0, 0
1: 1, 1, 0
2: 1, 0, 1
3: 0, 1, 1
4: -1, 1, 0
5: -1,0, 1
6: 0, -1,1

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.

Susumu

On Wed, Jul 22, 2009 at 4:40 PM, Helen Carlson <
Helen.Carlson at albertahealthservices.ca> wrote:

>  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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