Sample pipeline(.xml) to test generate snapshot

[Binita Shrestha]

Hello everyone,

I am trying to check  how snapshot are generated in case of image assessor. I have successfully created assessor using freesurfercommon plugin and would like to see how we can upload files under this assessor and can have a view of those on "View Snapshot" page as I can see gif files on that page.

In conclusion, I would like to understand how, snapshots are being generated.

It would be a great help, if anyone can provide a sample pipeline(xml) file, that contain steps, that does this thing for assessor and explain how it actually works .

Thanks 

[Herrick, Rick]

XNAT doesn’t generate snapshots for assessors. Prior to 1.8, XNAT used the AutoRun.xml pipeline to generate snapshots when image sessions were first archived. Now in 1.8 snapshots are generated on demand when first requested then stored as a resource on the scan for which the snapshot was generated. But this only applies to image sessions, not to assessors. I have very little experience with the FreeSurfer plugin so I’m not sure how snapshots are generated for those assessors, but it looks to me like it’s part of the FreeSurfer generation process:

 

• There’s a file in the FreeSurfer pipelines that CNDA uses called Freesurfer_Snapshots.xml.
• That is referenced by Freesurfer_5.3.xml to generate snapshots

 

This is about the extent of what I know about the FreeSurfer pipeline.

 

-- 

Rick Herrick

XNAT Architect/Developer

Computational Imaging Laboratory

Washington University School of Medicine

 

 

From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Binita Shrestha <binita....@snac.com.au>
Date: Thursday, July 15, 2021 at 10:18 PM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: [XNAT Discussion] Sample pipeline(.xml) to test generate snapshot

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[Binita Shrestha]

Hi Rick,

Thanks for sharing your understanding and sample pipeline.

I will definitely try out this pipeline for snapshot generation and see how it goes.

Thanks

--

Best Regards,

Binita Shrestha

Software Engineer

Sydney Neuroimaging Analysis Centre

94 Mallet Street, Camperdown, NSW   2050 Australia

E binita....@snac.com.au Mobile +61-449862369

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To view this discussion on the web visit https://groups.google.com/d/msgid/xnat_discussion/SN6PR02MB5118E64B6B7BC024742F3E86BD119%40SN6PR02MB5118.namprd02.prod.outlook.com.

[Binita Shrestha]

Hi Rick,

I copied necessary resource file and script file to run  Freesurfer_5.3.xml . I am getting error on ->step id="RUN_FS"

as shown on log file.

Can you tell me what I am doing wrong?

Thanks

--

Best Regards,

Binita Shrestha

Software Engineer

Sydney Neuroimaging Analysis Centre

94 Mallet Street, Camperdown, NSW   2050 Australia

E binita....@snac.com.au Mobile +61-449862369

This email and any files transmitted with it are confidential and may be privileged information that is intended only for the individual or entity named in the email address. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited. SNAC will NOT accept liability in connection with any computer virus, data corruption, delay or interruption and do not warrant that this email and its attachments are free from unauthorised amendment or other defect.