# PTOA-MRI-T1rho-and-T2star
Matlab files for processing PTOA knee MRI cartilage segmentations and calculating T1rho and T2*
A collection of Matlab M-files for reading Philips DICOM MRI T1rho and T2star knee image data, registering the spin lock or echo times using Melastix and elastix, reading OsiriX segmentation CSV files and calculating T1rho or T2star for regions of interest (ROIs).
The ROIs are based on the lateral and medial compartments of the femur and tibia. The compartments are divided into anterior (trochlea in the femur), central, and posterior regions. These cartilage ROIs are further divided into deep and superficial layers. Thus, there are 24 regions in each knee:
1. femur lateral trochlea deep ROI,
2. femur lateral trochlea superficial ROI,
3. femur lateral central deep ROI,
4. femur lateral central superficial ROI,
5. femur lateral posterior deep ROI,
6. femur lateral posterior superficial ROI,
7. femur medial trochlea deep ROI,
8. femur medial trochlea superficial ROI,
9. femur medial central deep ROI,
10. femur medial central superficial ROI,
11. femur medial posterior deep ROI,
12. femur medial posterior superficial ROI,
13. tibia lateral anterior deep ROI,
14. tibia lateral anterior superficial ROI,
15. tibia lateral central deep ROI,
16. tibia lateral central superficial ROI,
17. tibia lateral posterior deep ROI,
18. tibia lateral posterior superficial ROI,
19. tibia medial trochlea deep ROI,
20. tibia medial trochlea superficial ROI,
21. tibia medial central deep ROI,
22. tibia medial central superficial ROI,
23. tibia medial posterior deep ROI,
24. tibia medial posterior superficial ROI,
Please see PTOA_ImageAnalysisPipeline.pdf for a flowchart for the sequence of execution of Matlab M-files.
Please see the header comments in the M-files. Dependent functions are listed in the comments. There are a few helper M-files and a few unused M-files that are not required for the T1rho and T2* analyzes.
Note that the data must be in particular directories.
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用于处理PTOA膝关节MRI软骨分割和计算T1rho和T2的Matlab代码.zip
共109个文件
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用于处理PTOA膝关节MRI软骨分割和计算T1rho和T2的Matlab代码.zip (109个子文件)
cp_param.bat 1KB
seg_prois_bck2.m 31KB
seg_prois_old.m 30KB
seg_prois_bck.m 27KB
rd_m_dicom.m 25KB
mri_fitp.m 20KB
mri_fitps.m 19KB
pfits_chk.m 19KB
seg_prois.m 17KB
contact_chkp.m 16KB
mk_tplan_msks.m 16KB
dicom_chk2.m 16KB
mk_fplan_msks.m 15KB
psl_ana.m 13KB
pcmprt_ana.m 13KB
pcmprt_ana2.m 13KB
dicom_chk3.m 12KB
freg_axp26test.m 12KB
dicom_chk.m 12KB
intersections.m 12KB
pcmprt_ana_c.m 11KB
tibia_cs8.m 11KB
femur_rois.m 11KB
femur_rois2.m 10KB
mk_lay_msks.m 9KB
midline.m 9KB
dftregistration.m 8KB
mk_tri_2dfc.m 7KB
mk2_tri_2df.m 7KB
mk_tri_2dfw.m 7KB
dicom_lst2.m 7KB
mk_tri_2df.m 7KB
fem_plan.m 7KB
mk2_tri_2d.m 7KB
areaprop.m 7KB
mk_tri_2dc.m 6KB
mk_tri_2dw.m 6KB
plt_masks.m 6KB
T1r3d_calc.m 6KB
mk_tri_2d.m 6KB
psl_plt.m 6KB
pcmprt_plt.m 6KB
trim_seg.m 6KB
mk_tri4_2dc.m 5KB
f_cs_14.m 5KB
tib_plan.m 5KB
rd_prois.m 5KB
cyl_fit.m 4KB
rd_roi6.m 4KB
lisect4.m 4KB
rd_rois2.m 4KB
rd_rois.m 4KB
lsect5.m 4KB
lsect4.m 4KB
cr_mask2f.m 4KB
cr_mask2.m 3KB
InterX.m 3KB
lsect3.m 3KB
rb_trnsf.m 3KB
plt_csv6.m 3KB
plsect2.m 3KB
plane_fit.m 3KB
cr_maskfc.m 3KB
cr_masktc.m 3KB
mergeMAT.m 3KB
coord_tf.m 3KB
lsect2a.m 3KB
cr_maskf.m 3KB
cr_maskt.m 3KB
cyl_plt.m 2KB
in_tri2d.m 2KB
rd_pd_dicom.m 2KB
mtch_ends.m 2KB
li_clos.m 2KB
pts2lin.m 2KB
pt2line.m 2KB
cr_mask.m 2KB
plane_plt.m 2KB
dist2cyl.m 2KB
plsect.m 2KB
dftreg.m 2KB
plt_datsl.m 2KB
ptoa_demo.m 2KB
sl_dir.m 2KB
mk_inj_key.m 2KB
comb_dat.m 2KB
tri_area.m 2KB
fix_gap.m 2KB
lsq_build.m 1KB
near2.m 1KB
combine_shts3.m 1KB
combine_regs2.m 1KB
sl_info.m 1KB
plnorm.m 1KB
chk_gap.m 1KB
exp_fun1.m 1KB
rotxyz.m 1KB
run_seg_prois.m 552B
decomp.m 496B
run_rd_m_dicom.m 475B
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