[Loris-dev] importing MINC files into LORIS - registerFile.pl script ?

István Ákos Mórocz istvan.morocz at mcgill.ca
Wed Jun 28 12:07:47 EDT 2017 

yes, indeed, we will meet in 90min at NW125 :)
thank you for your informative emails, Mouna !
see you soon, bye, pisti

On Wed, 28 Jun 2017, Mouna Safi-Harab wrote:

> 
> Hi Sridar,
> 
> 
> Yes, I can confirm the script already exists. It is called 'batch_uploads_imageuploader'. It operates on a zip of DICOMs (not
> on MINCs) without using the imaging uploader GUI. It takes in a standard in (text file) of the entries (i.e. a zip of DICOM scans
> for a given candidate's MRI session) that need to be inserted into the database.
> 
> The scans should be placed on the filesystem and the text file would point to them, one at a time, and the above script will read
> the entries in the file, one line at a time, and process them for you from the backend without using the GUI.
> 
> 
> Details of how the script is launched and what additional inputs are required can be found here:
> 
> https://github.com/aces/Loris-MRI/pull/133
> 
> 
> 
> We have a meeting today (which I believe is to discuss this).
> 
> 
> - Mouna
> 
> ____________________________________________________________________________________________________________________________________
> From: Sridar Narayanan, Dr.
> Sent: Wednesday, June 28, 2017 11:43:11 AM
> To: Mouna Safi-Harab
> Cc: Istvan Akos Imre Morocz, Dr; Mouna Safi-Harab; loris-dev; Jordan Stirling
> Subject: Re: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ?  
> Hi Mouna,
> While the import/upload of DICOMs via the API will be a welcome addition to the LORIS tools, I think the immediate need is for batch
> upload of MRI files. Samir has indicated that this ability is already available (batch_upload_mri). Could you confirm whether this
> script operates only on MINC files, or DICOM as well? I think Pisti will need to know the details of how to run this script, as we
> will be importing tens of thousands of already-acquired MRI data into LORIS for the IPMSA project.
> 
> Thanks,
> 
> Sridar
> 
>
>       On Jun 28, 2017, at 7:24 AM, Mouna Safi-Harab <mouna.safi-harb at mail.mcgill.ca> wrote:
> 
> Hi Pisti,
> 
> 
> When you register a MINC file into the database, you should be able to store whatever MINC header is in the MINC file itself.
> So if the conversion from DICOM to MINC resulted in some loss, this will be reflected in the database (in other words, the
> database can only store the extent of what is in the MINC file, and comparing this to a DICOM starting point is dependent on
> the dcm2mnc conversion, not Loris).
> 
> 
> Regarding your second question, I know there is a few important things on the API development/improvement roadmap, one of
> which is uploading DICOMs and launching the pipeline through the API, however, I am not sure that end of summer is the
> projected completion time. I was under the impression that downloading DICOMs is more feasible by the end of the summer than
> uploading and inserting through the API, but I could be wrong. Xavier, Dave, and Samir which are on this email list can
> comment on the API timelines and priorities better than me. 
> 
> 
> - Mouna
> 
> ____________________________________________________________________________________________________________________________________
> From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of István Ákos Mórocz
> <istvan.morocz at mcgill.ca>
> Sent: Tuesday, June 27, 2017 1:58:57 PM
> To: Mouna Safi-Harab
> Cc: loris-dev; Jordan Stirling; Sridar Narayanan, Dr.
> Subject: Re: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ?  
> dear Mouna,
> 
> one of the key questions for us is if we loose essential information
> by importing MINC files into LORIS using the registerFile.pl script -
> as compared to using DCM files via the regular=manual LORIS way.  i
> assume here that we do a 'perfect' job outside LORIS when we convert
> DCM files to MINC files by using our own scripts.
> 
> then, we just heard this morning that the next LORIS version this
> summer will feature a DCM importing API - is that truly the case ?
> 
> bye, pisti
> 
> 
> On Thu, 22 Jun 2017, István Ákos Mórocz wrote:
> 
> > sounds good, dear Mouna - we will
> > give a try this coming tuesday in
> > the afternoon !  thanks for your
> > email !  bye, pisti
> >
> > On Thu, 22 Jun 2017, Mouna Safi-Harab wrote:
> >
> >> Hi Pisti,
> >> I will send a more detailed answer after the long weekend, but for now, the
> >> easiest way for you to know how the script functions is
> >> by simply typing at the command line (from where the MRI codebase
> >> directory):
> >> registerFile.pl -help
> >>
> >> This applies to almost all .pl scripts we have in the codebase.
> >>
> >> From that, you can see all the arguments and options you have to be able to
> >> run the script. But almost inevitably, you will have to
> >> write a wrapper script that is specific to your project and how you want to
> >> import the data (with some variable initialisation) that
> >> itself will call the registerFile.pl script.
> >>
> >> Give it a try, and we can talk more after the weekend.
> >>
> >> - Mouna
> >>
> >> On Tue, Jun 20, 2017 at 12:47 PM, István Ákos Mórocz
> >> <istvan.morocz at mcgill.ca> wrote:
> >>       dear LORIS developers,
> >>
> >>       as mentioned before in today's LORIS meeting, our group needs to
> >> learn
> >>       how to import some 42000 old MRI studies in MINC format into LORIS.
> >>
> >>       we learned in the mean time how to create CANDIDATE and VISIT entries
> >>       in LORIS via its jason API.  because there is no API for DICOM upload
> >>       (and because we may use our own dcm2minc pipeline) we were delighted
> >>       to hear from Mouna last week that one may go another route and import
> >>       MINC files actually directly into LORIS - so that subsequently Louis
> >>       Collins et al will be able to deal with QA and other processing
> >> steps.
> >>
> >>       question : can you refer us to weblinks, HOWTOs and any material on
> >>       using your registerFile.pl script and related environment so we get
> >>       this MINC upload mechanism working as soon as possible ?
> >>
> >>       thanks much, bye, pisti
> >>
> >>
> >>         ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._
> >>        '
> >>       :        http://noisis.com
> >>        `    istvan.morocz at noisis.com
> >>        :        +1-514-927-1169
> >>        :    istvan.morocz at mcgill.ca
> >>        :  http://cafe.spl.harvard.edu
> >>        ,    http://www.pistikem.org
> >>       :       pistikem at gmail.com
> >>        .
> >>         `~*-,._.,-*~'`^`'~*-,._.,-*~'`"
> >>
> >>
> >>
> >>
> >
> >  ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._
> > '
> > :        http://noisis.com
> > `    istvan.morocz at noisis.com
> > :        +1-514-927-1169
> > :    istvan.morocz at mcgill.ca
> > :  http://cafe.spl.harvard.edu
> > ,    http://www.pistikem.org
> > :       pistikem at gmail.com
> > .
> >  `~*-,._.,-*~'`^`'~*-,._.,-*~'`"
> 
>    ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._
>   '
> :        http://noisis.com
>   `    istvan.morocz at noisis.com
>   :        +1-514-927-1169
>   :    istvan.morocz at mcgill.ca
>   :  http://cafe.spl.harvard.edu
>   ,    http://www.pistikem.org
> :       pistikem at gmail.com
>   .
>    `~*-,._.,-*~'`^`'~*-,._.,-*~'`"
> 
> 
> 
>

   ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._
  '
:        http://noisis.com
  `    istvan.morocz at noisis.com
  :        +1-514-927-1169
  :    istvan.morocz at mcgill.ca
  :  http://cafe.spl.harvard.edu
  ,    http://www.pistikem.org
:       pistikem at gmail.com
  .
   `~*-,._.,-*~'`^`'~*-,._.,-*~'`"

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