Mining Whole Brain Segmentations

[hjmjohnson]

User Story

As DataCurator,
I want to identify whole brain size for a large number of data set from well defined atlases
so that further analysis can occur

Detailed Description

• Use atlases from /Shared/johnsonhj/2017Projects/20150416_MiniPigData/2017_ManualApprovedSegmentations directory as reference atlas
• Use module load BRAINSTools/20190415 and then BRAINSLandmarkInitializer -h to create initial transforms from each atlas brain to the new subject brain.
• Run AntsJointFusion to transfer labels from the 5 atlases to the other data sets.

Acceptance Criteria

• A single new brain is segmented
• A procedure to repeat for many datasets is identified

[KKnoernschild]

I am slightly confused on what I should do for the process here.

Do I need to create the landmark fcsv files for the 5 atlas files, or do those already exist?

[hjmjohnson]

You need to make the fcsv files for the 5 atlases as well.  You are the only person ever to define or identify landmarks in these datasets. Hans From: "notifications@github.com" <notifications@github.com> Reply-To: BRAINSia/SINAPSE <reply@reply.github.com> Date: Thursday, May 9, 2019 at 9:11 AM To: BRAINSia/SINAPSE <SINAPSE@noreply.github.com> Cc: Hans Johnson <hans.j.johnson@gmail.com>, Author <author@noreply.github.com> Subject: Re: [BRAINSia/SINAPSE] Mining Whole Brain Segmentations (#24) I am slightly confused on what I should do for the process here. Do I need to create the landmark fcsv files for the 5 atlas files, or do those already exist? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[KKnoernschild]

Shell script created that outputs resulting files to a subject-session file, that contains sub folders antsJointFusionResults (final result segmentationlabelmap), ImageFilesLinear , ImageFilesNearestNeighbor , and TransformFiles

Currently find all files and iterate through 2 of the ~120 scans, but this loop could be removed and then replaced with a file location, and make it transferrable for batch processing

The search radius is what dramatically effects the run time of each loop during the antsJointFusion .

a search radius of 3 results in a run time average of ~220 (3-4 minutes) seconds per subject, and a search radius of 5 had an average run time of ~850 seconds (14 minutes)

Search Radius of 3 took 520 seconds to run for 2 subjects.

[KKnoernschild]

• create a document with label/folder key to make files and results easily recognizable