[Loris-dev] [IPMSA] MINC extent

[Morales Pinzon, Alfredo]

Dear Cécile,

Thank you for explanation! Very helpful.

I was able to put the right values and get the query that we needed.

Regards,
Alfredo.
________________________________
From: Cecile Madjar <cecile.madjar at mcin.ca>
Sent: Tuesday, April 16, 2019 10:08 AM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Marciniak, Andrzej; Rozie Arnaoutelis; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D.; Samson Antel
Subject: Re: [Loris-dev] [IPMSA] MINC extent


        External Email - Use Caution

Dear Alfredo,

This can easily be done using an SQL query since every header present in the MINC files are inserted into the parameter_file table.

Quick review of the MRI tables' structure (tables that you will need to query):

  *   files => stores the path to the file and some basic information. Primary key = FileID
  *   parameter_type => stores the data dictionary of LORIS. Primary key = ParameterTypeID (all MINC header names can be found in this table when you add (WHERE SourceFrom="parameter_file")
  *   parameter_file => stores all files MINC header values. Foreign keys to the files and parameter_type tables being the FileID and ParameterTypeID columns of parameter_file. The Value column would store the MINC header value

So basically, to query the files matching a specific value for a MINC header, you would use a query like this one:

SELECT File, Value
FROM files f
  JOIN parameter_file pf USING (FileID)
  JOIN parameter_type pt USING (ParameterTypeID)
WHERE
  pt.Name="YOUR MINC HEADER NAME HERE"
  AND pf.Value="THE VALUE YOU WANT TO RESTRICT THE QUERY ON"

In blue are the part that you will need to populate based on what you are looking for. For example, if you want to select all files with a repetition time of 2000ms, you would use the following values:

  *   pt.Name="acquisition:repetition_time"
  *   pf.Value="2000"

Hope this helps. Let me know if something is not clear or if you have additional questions.

Best,

Cécile


On Mon, Apr 15, 2019 at 6:17 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LORIS-dev team,

We have found an issue with some images where the created MINC file in LORIS only contains 1 slice. We have identified the potential error, which comes from the DICOM files, but we would like to track the images imported into LORIS having this problem. Is the information about the extend of the images saved in the database? What would be the best strategy to find these images.

Best regards,
Alfredo.

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

_______________________________________________
Loris-dev mailing list
Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190417/e71b5f55/attachment.html>