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

Thu Jul 23 19:21:22 EDT 2009

That's a good question. I remember that I tried to divide them simply based
on the file name but it didn't work.

If you could ftp the data to us, we can take a look at the data to see if we
can easily write a code to separate them.

Susumu

On Thu, Jul 23, 2009 at 3:49 PM, Helen Carlson <
Helen.Carlson at albertahealthservices.ca> wrote:

>  Hi Susumu,
> Thank you very much for all your help.
>
> Since we do use oblique angles I am currently exploring option 5-1 below.
> My question is: 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.
>
> Thank-you again.
> Helen.
>
>
>  *Helen Carlson*, Ph.D.
> Neuropsychology
> Department of Neurosciences
> Alberta Children's Hospital
>
>   ------------------------------
> *From:* mristudio-users-bounces at mristudio.org [
> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [
> susumu at mri.jhu.edu]
> *Sent:* July 22, 2009 8:01 PM
> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support
> *Subject:* Re: [Mristudio-users] How to Process Siemens Mosaic files in
> DTIStudio?
>
>  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
>> _______________________________________________
>> Mristudio-users mailing listMristudio-users at mristudio.org <http://lists.mristudio.org/mailman/listinfo/mristudio-users>http://lists.mristudio.org/mailman/listinfo/mristudio-users
>>
>>
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