Code cleanup, documentation, and maintenance (2023):
As CAT12 has become more or less mature it is time to document and clean up unused functions, uncommented code blocks and connected or outdated parameters. This issue should help to organise this process.
Documentation:
[x] cat_vol_approx. + Add a new simple version and a unit test. ... Although the new recursive function supports quite good values and nicer maps, the test with Collins and HR075 has not shown the desired improvement so far. The figures show the results of high- and low-frequency test cases and HR075, whereas the table shows the values of all unit tests.
method
res2
res
nn4
nn1
nno4
nno1
mean
2.4690
2.4943
2.5988
2.5458
3.0086
2.5376
std.
3.0776
3.0658
3.1428
3.1616
3.6160
3.0696
time
0.4927
0.4748
0.5583
1.1874
0.1967
1.5742
[x] cat_vol_resize. Improve documentation and help. Add unit test.
Cleanup:
[x] KAMAP: Remove alternative SPM-preprocessing AMAP pipeline prototype (cat_main_kamap/extopts.segmentation.spm_kamap).
[x] APP: Removal of unused APP cases (and connected functions) and reduction of cat.extopts.APP parameter to simple yes/no setting. After revision, the APP full and rough (new) were removed but the APP light option was kept. APP light is an iterative call of the SPM segmentation but only to remove inhomogeneities and works quite well also it is a bit slow. The function parameters were lightly simplified and tested (Collins/HR075).
[x] cat_vol_pbt3: Remove failed development function and parameters.
[x] cat_vol_pbtp2: currently not used but was maybe more stable - need further tests - no, it is worse >> removed.
[x] cat_vol_LASs: Simplified version used for PD/T2 processing in cat_main. >> Replace later with an even simpler LAS version?
[x] multiTPM: Remove support of multiple TPMs with automatic selection as it is not further used.
[x] Fast surface creation: Remove fast surface processing without registration as the CS3 pipeline takes only a bit longer.
[x] cat_vol_LAS2: This is a reworked version of cat_vol_LAS with addition comments and smaller updates. I.e. it should replace the old version.
Maintenance:
Further things we could think about are:
[x] Dartel: Maybe remove the Dartel support in a future version? - Better not because of test, own templates and compatibility.
Code cleanup, documentation, and maintenance (2023): As CAT12 has become more or less mature it is time to document and clean up unused functions, uncommented code blocks and connected or outdated parameters. This issue should help to organise this process.
Documentation:
Cleanup:
Maintenance: Further things we could think about are: