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This page is readable only by those in the LcnGroup.
Author(s): Nick Schmansky
See: Samseg
Samseg Aseg Testing
This page documents one front of the work on Samseg, where testing of a version of Samseg operating on T1-weighted input and using the existing RB FS atlas, is conducted to compare its performance against the existing FreeSurfer v6.0 subcortical segmentation processing stream. Initial work was conducted in an evaluation task: SamsegEvaluationMarch2016. The current work pertaining to this page extends that work by:
Creation of a test cycle allowing the comparison of a subject run of Samseg (which is under algorithmic development) to the FS aseg results from v6 for that subject. The test cycle should generate reports on a run, allowing for debug, and evaluation of performance to meet, initially, the aims of the CorticoMetrics grant aims (ie, an accelerated FS based on T1 input only)
- Creation of a data set which includes enough subjects to cover the wide variety of possible inputs. Starting with Buckner40 and ADNI60, and continuing with many others, particularly subjects having extension neck in the FOV, as well as 'tough cases' both in terms of registration and segmentation.
- Documentation of design decisions.
Test Data
The test subjects and scripts are located here: /cluster/fsm/users/samseg
Test sets used to compare samseg results will include:
- Buckner40 - processed by FS v6, where aseg's have been manually inspected as part of FS release testing
- ADNI60 - processed by FS v6, where aseg's have been manually inspected as part of FS release testing
Siemens13 - 13 manually labeled subjects scanned on Siemens Sonata (currently used in testing the FS atlas: AsegTestNotes)
GE14 - 14 manually labeled subjects scanned on GE Signa (currently used in testing the FS atlas: AsegTestNotes)
- ADNI-FS53 - processed by FS 5.3, and QA'd by Tian Ge (but asegs not each manually inspected)
OutlierSet - consisting of subject scans known to be problematic (lots of neck, skewed placement in scanner, etc.)
- IXI, HCP, OASIS, HABS, BRAINS, Mindboggle-101, BGSP - all publicly available datasets where the intent is to process by FS v6 to include in the aseg test set.
- ANDI-Long - test-retest set
- Bammer120 - test-retest set