[Loris-dev] Imaging Browser Headers and Data Query Tool

[Michael Joseph]

Hi Mouna,


Thank you! That worked. The headers are showing up now. For the 'Number of volumes' field, is that related to time or is it the number of slices taken? It's only being reported for the DTI and fMRI scans.


I tried updating CouchDB as I thought the missing headers might be related but this didn't fix that issue.


Thanks,

Michael


________________________________
From: Mouna Safi-Harab <mouna.safi-harb at mail.mcgill.ca>
Sent: June 6, 2017 2:50:21 PM
To: Michael Joseph; loris-dev at bic.mni.mcgill.ca
Subject: Re: Imaging Browser Headers and Data Query Tool


Hi Michael,


I will tackle the first item in your email, and someone else from the Loris team will get back to you on the second.


The headers are not showing up because they likely are not populated in the parameter_file table.

I think your issue is coming from the MYSQL version you have. I am assuming you have MYSQL 5.7 and as you are inserting scans, you are getting a message as follows:

DBD::mysql::db do failed: Data too long for column 'Value' at row 334 at /data/braincode/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 753.

This error results in the parameter_file table not populating your entries.


A quick fix would be to alter the parameter_file Value column type to go from Text to LongText. You can give it a try and let me know if this solves your issue (I tested it locally and it seems to work), but I need to run this fix by the Loris-MRI group. Once that is done, we will hopefully issue a fix in the next release.


- Mouna




________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Michael Joseph <michael.joseph at sickkids.ca>
Sent: Tuesday, June 6, 2017 11:31:44 AM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Imaging Browser Headers and Data Query Tool


Hi Loris dev team,


I have two queries:


1) I've been uploading images to Loris though the back-end using the dicomTar.pl and tarchiveLoader scripts. I noticed that the headers for each scan in the Imaging Browser module are incomplete. Only the 'Output Type', 'Space', 'Protocol' and 'Inserted Date' fields show up correctly. The 'Voxel Size', 'Echo Time', 'Rep Time', Slice Thick' and 'Number of volumes' all report 0. The rest of the fields are empty. Did I miss a step that populates the headers?


2) I also recently set up the Data Query Tool. For the 'mri_data' instrument, the only filter I get is 'QCComment'. The 'demographics' instrument is working properly. Do you have any ideas why the rest of the filters don't appear?


Thank you,


Michael

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