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

Fri Apr 30 17:44:42 EDT 2010

try SPM, it's the only program that allows me to convert my *.MR images from
a 3T GE scanner.

it's called dicom import.

sophie

also, maybe try Mango?
http://ric.uthscsa.edu/mango/

On 30 April 2010 17:15, Mithra <mithra at mail.utexas.edu> wrote:

> 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
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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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