[Mristudio-users] Importing Siemens slice dicom images to dtistudio

Fri Apr 30 17:15:24 EDT 2010

Hello,
I have a similar issue. I have DTI data collected long ago from a Siemens
Trio scanner. The raw data is in '.dat' format. Is there a way to convert
the files into dicoms or Nifti files?

Thank you for your help.

Regards,
Mithra.

On Fri, Apr 30, 2010 at 4:03 PM, Pieter Vandemaele <
pieter.vandemaele at ugent.be> wrote:

> You can use the free software MRIConvert (
> http://lcni.uoregon.edu/~jolinda/MRIConvert/<http://lcni.uoregon.edu/%7Ejolinda/MRIConvert/>)
> or XMedCon (http://xmedcon.sourceforge.net/) to do file
> conversion/splitting.
>
> Best
>
> Pieter
>
> Op 30-apr-2010, om 21:31 heeft Ashtari, Manzar het volgende geschreven:
>
> There is no problem reading the siemens mosaic dicom images into the
> DTIStudio.  Naama may want the individual images for something else.  Or
> she may have gotten the images on a CD and exactly what you said had
> happened and she does not know what happened to the rest of the images.
> Best,
>
> MA
> *
>
> *
> ------------------------------
> *From:* mristudio-users-bounces at mristudio.org [
> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [
> susumu at mri.jhu.edu]
> *Sent:* Friday, April 30, 2010 3:29 PM
> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang
> *Subject:* Re: [Mristudio-users] Importing Siemens slice dicom images to
> dtistudio
>
> Hmmmm, reading the Mosaic into DtiStudio let you see individual images. You
> can save them as separate raw or Analyze files. If you want DICOM, I thought
> there was a way. Hangyi, I thought there was a DICOM save option?
>
> On Fri, Apr 30, 2010 at 3:23 PM, Naama Barnea-Goraly <naamab at stanford.edu>
>  wrote:
>
>>
>> Manzar is right, I would like to see the images individually - like the GE
>> output. Susumu's reply makes me think I am missing something. Right now I
>> can only look at a whole slice so I can't compare the different repetitions,
>> also in the image window I can only see the whole slice in axial view (2D).
>> Anyway I can view this scan differently?
>>
>> Thanks,
>>
>> Naama
>>
>>
>>
>>
>>
>>
>>
>> On Apr 30, 2010, at 11:37 AM, susumu mori wrote:
>>
>> Oh I see. I'm not sure why Naama wants it....
>>
>> On Fri, Apr 30, 2010 at 2:34 PM, Ashtari, Manzar <ASHTARI at email.chop.edu>
>>  wrote:
>>
>>> I know what Naama is asking for.  Siemens images come in mosaic form and
>>> she wants to have them none mosaic.  I know you can convert them on the
>>> scanner but don't know of any program that does it in a lab setting.
>>>
>>>
>>> Best,
>>>
>>> MA
>>> *
>>>
>>> *
>>> ------------------------------
>>> *From:* mristudio-users-bounces at mristudio.org [
>>> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [
>>> susumu at mri.jhu.edu]
>>> *Sent:* Friday, April 30, 2010 12:25 PM
>>> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang
>>> *Subject:* Re: [Mristudio-users] Importing Siemens slice dicom images to
>>> dtistudio
>>>
>>> Naama,
>>>
>>> I'm not exactly sure about what you are asking but maybe related to what
>>> I experienced in the past?
>>>
>>> For Siemens, GE, and Philips, I got an impression that you need a
>>> research agreement to store DICOM files into separate directories based on
>>> imaging type such as T1, T2, DTI. If you run scans and burn a CD for
>>> clinical purpose, you find DICOM files all mixed up in 1 or multiple
>>> directories with a generic names, from which it is very difficult to sort.
>>> These CD usually includes a DICOM viewer and you need to use it for the
>>> viewing purpose.
>>>
>>> So, I would first check if your scanner has an option to save DICOM in
>>> separate directories based on the modalities. If not, we wrote a small
>>> program to sort out the clinical DICOM files. We don't use this very often
>>> and may not work for some type of operating systems, but you can at least
>>> give it a try. Please contact Hangyi if you want it.
>>>
>>> Susumu
>>>
>>>
>>> On Fri, Apr 30, 2010 at 10:46 AM, Ashtari, Manzar <
>>> ASHTARI at email.chop.edu> wrote:
>>>
>>>> Yes you will have a separate series listed along with others.
>>>> Best,
>>>>
>>>> MA
>>>> ________________________________________
>>>> From: mristudio-users-bounces at mristudio.org [
>>>> mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly
>>>> [naamab at stanford.edu]
>>>> Sent: Friday, April 30, 2010 10:16 AM
>>>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>>>> Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to
>>>>  dtistudio
>>>>
>>>> Thank you - is there a way to separate them off the scanner?
>>>>
>>>> Thanks,
>>>>
>>>> Naama
>>>>
>>>>
>>>>
>>>> On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote:
>>>>
>>>> > This is done as an option on the scanner. You can also perform this
>>>> > after the images are reconstructed.
>>>> > Best,
>>>> >
>>>> > MA
>>>> > ________________________________________
>>>> > From: mristudio-users-bounces at mristudio.org [
>>>> mristudio-users-bounces at mristudio.org
>>>> > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu]
>>>> > Sent: Friday, April 30, 2010 9:41 AM
>>>> > To: DiffeoMap Questions/Support DTI Studio ROI Editor
>>>> > Subject: [Mristudio-users] Importing Siemens slice dicom images to
>>>> > dtistudio
>>>> >
>>>> > The output from the Siemens scanner are slice dicom images. How do I
>>>> > separate them into individual images like the ones we get from GE?
>>>> >
>>>> > Thanks,
>>>> >
>>>> > Naama
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > _______________________________________________
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>>>>
>>>> Naama Barnea-Goraly M.D.
>>>> Instructor
>>>> Center for Interdisciplinary Brain Sciences Research
>>>> Stanford University Division of Child and Adolescent Psychiatry
>>>> 401 Quarry Rd. MC 5795
>>>> Stanford University School of Medicine
>>>> Stanford, CA  94305-5795
>>>> Phone: (650) 736-1874, fax: (650) 724-4794
>>>>
>>>>
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>>>>
>>>>
>>>>
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>>>
>>>
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>>
>> Naama Barnea-Goraly M.D.
>> Instructor
>> Center for Interdisciplinary Brain Sciences Research
>> Stanford University Division of Child and Adolescent Psychiatry
>> 401 Quarry Rd. MC 5795
>> Stanford University School of Medicine
>> Stanford, CA  94305-5795
>> Phone: (650) 736-1874, fax: (650) 724-4794
>>
>>
>> CONFIDENTIALITY NOTICE:  This e-mail communication and any attachments may
>> contain confidential information for the use of the designated recipients
>> named above.  If you are not the intended recipient, you are hereby notified
>> that you have received this communication in error and that any review,
>> disclosure, dissemination, distribution or copying of it or its contents is
>> prohibited.  If you have received this communication in error, please notify
>> Stanford Medical Center immediately by telephone at (650) 725-5722 and
>> destroy all copies of this communication and any attachments.  Thank you.
>>
>>
>>
>>
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