Re: Nifti data type
Tim Olsen
Maria,
Importing Nifti data into XNAT can be done, but can be a challenge due to the limited fields available in the Nifti headers.
Which fields are you pulling from your Nifti? In particular, have you found a way to map your Nifti files to specific series in the DICOM sense? How do you know which files are for scan 1 vs scan 2?
Will you also be importing DICOM? Will you be operating from a script or from within the website?
Tim
On Wednesday, April 24, 2013 6:09:47 AM UTC-5, Maria Moloci wrote:
Hello everyone!
I am trying to make a new Data type for Nifti images which includes all the Nifti header fields.
- how saves Xnat the header information from Dicom images in the database? Does it use a Pipeline? Where can I find these Pipeline or an executable which takes the header information and bring them in the database?
-which procedure should I use to save the Nifti header fields in the database?
I'm happy about any answer or idea to resolve these problem
Maria Moloci
Hello Tim,
I want to get all the header-fields from the Nifti files and push them in the Xnat. I want to use a script to import the Nifti files with additional project related information. I don't have specific series for the Nifti files, therefore, a mapping to DICOM series is not necessary.
I also want to import Dicom files.
Thank you for your response,
Maria
Tim Olsen
I’d recommend loading your DICOM first, so that you can see the structure which it creates and place your NIfTI where you want it. In XNAT, imaging data is organized into imaging sessions (like a DICOM study). Each imaging session has a collection of scans (like a DICOM series). An imaging session can also have files associated at the session level (not for specific scans), generally called session resources. Or, you can create image session assessments which also relate to the imaging session but include additional details about the assessment performed.
How are you planning on using the header values which you store in XNAT? Do you want to go to a web page and view a list of all the header values in your database? Or, do you want to retrieve them on a case-by-case basis? I can make a better recommendation of how to store the data, if I know how you want to retrieve/use it.
Tim
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Maria Moloci
Sent: Monday, May 13, 2013 6:11 AM
To: xnat_di...@googlegroups.com
Subject: [XNAT Discussion] Re: Nifti data type
Hello Tim,
I want to get all the header-fields from the Nifti files and push them in the Xnat.I also have other fields in my new data type, which are important for the project. I don't have specifc series for the Nifti files, therefore, a mapping to DICOM series is not neccessary.
I also want to import Dicom files and I will use a script.
Thank you for your response,
Maria
Am Dienstag, 30. April 2013 20:57:12 UTC+2 schrieb Tim Olsen:
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Maria Moloci
I want to get a web page with all the nifti-header values from the database. Thank you for your help.
Maria
Tim Olsen
Do you want all of the nifti-header values for an individual imaging session, or for all imaging sessions in the database in one big table?
Visit this group at http://groups.google.com/group/xnat_discussion?hl=en-US.
Maria Moloci
I spoked with Romanus and Thomas, the team leaders for the Xnat-Project where I work now and they actually want to retrieve the Nifti-header values in a case-by-case study, just like the Dicom-header values in the Xnat: ->Project
->Subject
-> Imaging Session: Nifti Images, list with Nifti header values for these specific Imaging Session
Thank you for your help,
Maria