[Neuroimaging] Discourse category for DICOM discussions

[Brendan Moloney]

Hi,


Thanks for the tip for handling Bruker data.  We have been using a mix of home grown code and Bruker2Nifti.


Brendan Moloney
Senior Research Associate
Advanced Imaging Research Center
Oregon Health Science University
________________________________
From: Neuroimaging <neuroimaging-bounces+moloney=ohsu.edu at python.org> on behalf of VRomain <romain.valabregue at upmc.fr>
Sent: Tuesday, July 13, 2021 3:19:38 AM
To: neuroimaging at python.org
Cc: Julien Lamy
Subject: [EXTERNAL] Re: [Neuroimaging] Discourse category for DICOM discussions

Hi there


may be an other link worth to look at :

Julien which is not on this list ( lamy at unistra.fr ) have made nice
development on dicom parsing

https://github.com/lamyj/odil/

and for conversion of Bruker raw data to dicom file (and then dicom to
nifti)

and https://github.com/lamyj/dicomifier/


It is quite amazing to realize that Bruker, is not able to give us a
decent dicom output, with all information one needs (like direction of
diffusion, ...),

I was used to dcmstack, but for my bruker raw data, this is the tool to
go ...


Romain



On 10/07/2021 18:09, Matthew Brett wrote:
> Hi Steve,
>
> Some sparse notes here:
>
> https://docs.google.com/document/d/1Ca999GAx1qfCT0Hw5JRlJSEJeVTRDYaIg1h1LWbgYoo/edit?usp=sharing
>
> The next plan was to have a show-and-tell session where we go over the
> main parts of the various Python libraries covering DICOM in
> neuroimaging, which we so far have as:
>
> dicom_parser
> dcmstack
> Nibabel/nicom
>
> All welcome, as usual; any other suggestions welcome.  We haven't got
> a time yet - I think Zvi had kindly agreed to poll and set that up
> next week.
>
> Cheers,
>
> Matthew
>
> On Sat, Jul 10, 2021 at 5:06 PM Steve Pieper <pieper at isomics.com> wrote:
>> Hi Mathew and Satra -
>>
>> I'm sorry I couldn't attend the meeting yesterday, but I look forward to this further discussion.  Are there any notes from the meeting?
>>
>> Best,
>> Steve
>>
>> On Sat, Jul 10, 2021 at 11:54 AM Matthew Brett <matthew.brett at gmail.com> wrote:
>>> Hi,
>>>
>>> Ah - sorry - I didn't realize Neurostars was a Discourse instance - I
>>> hadn't looked for ages.  No, no reason, let's move there.  How do I
>>> create a new category?  Is there a system for collecting / archiving
>>> the post data so that we can replicate it if there's a problem?
>>>
>>> Cheers,
>>>
>>> Matthew
>>>
>>>
>>>
>>> On Sat, Jul 10, 2021 at 4:15 PM Satrajit Ghosh <satra at mit.edu> wrote:
>>>> hi matthew,
>>>>
>>>> any reason not to use neurostars for this (which is a discourse platform)? a number of neuroimaging software discussions are already happening there, including questions about nibabel and dicom conversion tools.
>>>>
>>>> cheers,
>>>>
>>>> satra
>>>>
>>>> On Sat, Jul 10, 2021 at 10:43 AM Matthew Brett <matthew.brett at gmail.com> wrote:
>>>>> Hi,
>>>>>
>>>>> We had a good discussion yesterday about what to do next with Python and DICOM.
>>>>>
>>>>> To keep the discussion going, while not overloading your inboxes, I've
>>>>> asked Discourse for a Nipy Discourse instance, and I've made a
>>>>> category for the DICOM discussions, here:
>>>>>
>>>>> https://nipy.discourse.group/c/python-dicom
>>>>>
>>>>> Can I suggest that we move the DICOM discussions to that category?
>>>>> Then we can feed back here, from time to time.
>>>>>
>>>>> The Discourse category is all public, so you can always go and see
>>>>> what we are up to by following the link.  For those new to Discourse,
>>>>> it's a rather nice Forum-like system that has good email integration,
>>>>> and Markdown editing, so it's a nice way of making well-formed,
>>>>> publicly searchable messages and discussions, that you can use via
>>>>> email if you want.
>>>>>
>>>>> If anyone wants new categories or admin permissions on the Discourse
>>>>> instance, just let me know.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Matthew
>>>>> _______________________________________________
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>>>>> Neuroimaging at python.org
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