Create sample data from all the sources

[tdowrick]

In GitLab by @DavidPerez-Suarez on Nov 23, 2018, 15:58

What are the sources and their format?

source	format
Clinical data	text
MRI data (pre/post)	DICOM or nii
CT	DICOM or nii
Tractography	nii
Tumour volume (segmentation)	nii
Stylus tracking data	4x4 Matrix
Intra op neuromonitoring data	?
SureTrack tracking for US	4x4 Matrix
UltraSound data (image/video)	PNG/AVI or equivalent

[tdowrick]

In GitLab by @JonathanShapey on Nov 28, 2018, 14:24

changed the description

[tdowrick]

In GitLab by @JonathanShapey on Nov 28, 2018, 14:24

MR and CT data- DICOM (but could also be nifti) Diffusion data (DWI and DTI)- currently generated in .mif format but I'm not sure this is supported (see link below) so we can convert this to nifti Tumour volume- nifti All tracking data will come through slicer anyhow but originally comes from the Stealthstation in text format Intra-operative monitoring- need to check but I think this is text based & .bmp Ultrasound-

[tdowrick]

In GitLab by @JonathanShapey on Nov 28, 2018, 14:28

Useful links:

http://perk-software.cs.queensu.ca/plus/doc/nightly/user/DeviceBkProFocus.html

https://www.slicer.org/wiki/Documentation/4.8/SlicerApplication/SupportedDataFormat

I'm waiting to hear back from the neurophysiology team regarding the data format for the neuromonitoring data. At best we will live stream the video feed and link to the stimulator tracking data. At worst, we will upload a screen shot (.bmnp or .jpeg) of the acquired neurophysiology data and link to the tracking data point.

[tdowrick]

In GitLab by @JonathanShapey on Nov 28, 2018, 14:28

closed

[tdowrick]

In GitLab by @DavidPerez-Suarez on Dec 5, 2018, 16:37

reopened

[tdowrick]

In GitLab by @JonathanShapey on Dec 14, 2018, 13:51

Contacted Micromed who make the NIM Eclipse neuromonitoring system. The UK technical lead thinks that it is possible to stream the data but he is checking with his US counterparts and will let me know next week what format the data is in

[tdowrick]

In GitLab by @JonathanShapey on Dec 14, 2018, 16:50

@JonathanShapey @RemiDelaunay will create samples of each data source

[tdowrick]

In GitLab by @DavidPerez-Suarez on Jan 14, 2019, 10:56

@RemiDelaunay and @JonathanShapey created the following during the first week of January:

• US images of @RemiDelaunay's forearm (now also stored on RDS). The sequences folder corresponds to data that can be open with the sequence module and includes the probe tracking and imaging data. I also acquired some ultrasound images alone.
• MR and tractography data. It includes T1 and T2 MR data plus tumour segmentations for both.

@RolandGuichard has been familiarising with the data.

[tdowrick]

In GitLab by @DavidPerez-Suarez on Feb 18, 2019, 10:30

@RolandGuichard to put it on the wiki/docs

[tdowrick]

In GitLab by @ThomasDowrick on Feb 28, 2019, 14:44

changed the description

[tdowrick]

In GitLab by @DavidPerez-Suarez on Apr 8, 2019, 08:24

closed