Getting all DICOM files from a scan at once using pyxnat

[Andrey Fedorov]

Hi,

I am trying to work around the bug described here: https://groups.google.com/d/topic/xnat_discussion/zV5xDIXNrWU/discussion

I was told it is possible to get all the DICOM files for a given scan at once. Can someone tell me how this can be done using pyxnat?

I tried

 project.subject(s).experiment(e).scan(s).resources('DICOM').get(path)

but this does not seem to work (for some scans, I am getting a zip file with a number of files, each called 'DICOM', and the number of those files does not match the expected number of DICOM files).

Is there a way to do this?

AF

[Herrick, Rick]

Andrey,

 

I haven’t been ignoring you but simply haven’t had time to look into this. Can you send me more of the code creating the objects for your subject, experiment, etc.?

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[Just, David J. (Dave)]

There are times when it is more convenient to NOT use pyxnat.  This is one of those times:
Using this URL format to a CURL command will get you a zip of just the dicom:

URL="${XNAT_SERVER}/data/projects/${XNAT_PROJECT}/subjects/${SUBJECT}/experiments/${STUDY}/scans/${SERIES}/resources/DICOM/files?format=zip"

If you want to stay inside of python, the “requests” library is also very handy in a few cases.

On 1/16/13 4:39 PM, "Herrick, Rick" <herr...@mir.wustl.edu> wrote:

[Chen Yang]

Hi, 

Here is the way that we are using to download all the DICOM files for a given scan at once by using pyxnat. 

scans = project.subject(s).experiment(e).scans()

scans.dwonload(tempDir, type=seriesNumber,extract=True) # download all the DICOM file of  the given seriesNumber scan to tempDir and extract them. 

Good luck!

Chen

AF

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