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

Naama Barnea-Goraly naamab at stanford.edu
Fri Apr 30 18:28:02 EDT 2010 

We had a similar issue with GE data and used Osirix to extract the  
files we needed (it is not the issue I currently have with Siemens  
data).



On Apr 30, 2010, at 2:15 PM, Mithra 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/ 
> ) 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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>>
>> 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.
>>
>>
>>
>>
>> _______________________________________________
>> Mristudio-users mailing list
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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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