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moloney / dcmstack

DICOM to Nifti conversion with meta data preservation
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proper way to install #21

Closed ag-bell closed 10 years ago

ag-bell commented 10 years ago

What is the recommended way to install dcmstack? I downloaded using the git clone protocol. Then ran "python setup.py install". The behavior seemed to be that an egg was created in site-packages. Also, in my Anaconda/Scripts directory I see dcmstack-script.py and dcmstack.exe and dcmstack.exe.manifest.

The problem, when in python, I can't import dcmstack. It doesn't find it. Also, when I try running easy_install on the egg, it says it can't find a setup script in the egg. Thanks for any help, probably user error;)

Chris

moloney commented 10 years ago

Hi, sorry for the delayed response.

Typically you would run easy_install on the source tarball. But this should be equivalent to "python setup.py install". I am not sure if your problem is specific to anaconda?

ag-bell commented 10 years ago

Hmm. Now it seems to install correctly no matter if I am in Anaconda or outside. Not sure what I did wrong before.

Is the current best practice for using dcmstack within nipype, to use interfaces to the dcmstack command line? It sounds like dcmstack/nibable integration is still a work in progress? One of the things I want to do, is to get the dicom header information into a relational or nosql database, have you done this before? Thanks for all the help.

On Tue, Mar 11, 2014 at 12:17 PM, moloney notifications@github.com wrote:

Hi, sorry for the delayed response.

Typically you would run easy_install on the source tarball. But this should be equivalent to "python setup.py install". I am not sure if your problem is specific to anaconda?

Reply to this email directly or view it on GitHubhttps://github.com/moloney/dcmstack/issues/21#issuecomment-37337921 .

nicholsn commented 10 years ago

wrt persisting the dicom header in a nosql db, it's pretty straight forward to load the dcmstack JSON NIfTI extension into mongodb using pymongo ( http://api.mongodb.org/python/current/api/bson/json_util.html)

On Tue, Mar 11, 2014 at 12:54 PM, Christopher J Bell < notifications@github.com> wrote:

Hmm. Now it seems to install correctly no matter if I am in Anaconda or outside. Not sure what I did wrong before.

Is the current best practice for using dcmstack within nipype, to use interfaces to the dcmstack command line? It sounds like dcmstack/nibable integration is still a work in progress? One of the things I want to do, is to get the dicom header information into a relational or nosql database, have you done this before? Thanks for all the help.

On Tue, Mar 11, 2014 at 12:17 PM, moloney notifications@github.com wrote:

Hi, sorry for the delayed response.

Typically you would run easy_install on the source tarball. But this should be equivalent to "python setup.py install". I am not sure if your problem is specific to anaconda?

Reply to this email directly or view it on GitHub< https://github.com/moloney/dcmstack/issues/21#issuecomment-37337921>

.

— Reply to this email directly or view it on GitHubhttps://github.com/moloney/dcmstack/issues/21#issuecomment-37341925 .