diff --git a/docs/404.html b/docs/404.html index b754d332..cdfb66a3 100644 --- a/docs/404.html +++ b/docs/404.html @@ -39,7 +39,7 @@
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index 60e9cd7a..2313e1d5 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -17,7 +17,7 @@ diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 6158eea7..463db377 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ diff --git a/docs/articles/abfit-baseline-opts.html b/docs/articles/abfit-baseline-opts.html index d760cc8f..c77d5f9a 100644 --- a/docs/articles/abfit-baseline-opts.html +++ b/docs/articles/abfit-baseline-opts.html @@ -40,7 +40,7 @@ diff --git a/docs/articles/index.html b/docs/articles/index.html index f2b1c0a5..c89625ef 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ diff --git a/docs/articles/spant-basis-simulation.html b/docs/articles/spant-basis-simulation.html index a7bae86c..ec37a6fb 100644 --- a/docs/articles/spant-basis-simulation.html +++ b/docs/articles/spant-basis-simulation.html @@ -40,7 +40,7 @@ diff --git a/docs/articles/spant-intro.html b/docs/articles/spant-intro.html index 9885ae90..a73fc35c 100644 --- a/docs/articles/spant-intro.html +++ b/docs/articles/spant-intro.html @@ -40,7 +40,7 @@ @@ -194,54 +194,54 @@
fit_res$res_tab
-#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr GABA
-#> 1 1 1 1 1 1 0 8.228814e-06 3.54833e-05 4.020309e-05 1.706751e-05
+#> X Y Z Dynamic Coil X.CrCH2 Ala Asp Cr GABA
+#> 1 1 1 1 1 1 0 8.22876e-06 3.54834e-05 4.020301e-05 1.706748e-05
#> Glc Gln GSH Glu GPC Ins
-#> 1 2.442178e-06 3.029766e-06 2.227788e-05 6.499653e-05 1.603289e-05 5.902969e-05
-#> Lac Lip09 Lip13a Lip13b Lip20 MM09 MM12
-#> 1 5.818682e-06 2.362971e-05 2.635459e-06 0 0 9.887561e-06 6.54698e-06
+#> 1 2.441973e-06 3.029672e-06 2.227785e-05 6.499641e-05 1.603287e-05 5.902947e-05
+#> Lac Lip09 Lip13a Lip13b Lip20 MM09 MM12
+#> 1 5.818711e-06 2.362975e-05 2.635412e-06 0 0 9.887518e-06 6.546981e-06
#> MM14 MM17 MM20 NAA NAAG PCh
-#> 1 2.599935e-05 2.245507e-05 9.207422e-05 5.981785e-05 1.556185e-05 0
-#> PCr sIns Tau tNAA tCr tCho
-#> 1 2.101291e-05 6.508652e-06 0 7.53797e-05 6.121601e-05 1.603289e-05
+#> 1 2.599936e-05 2.245502e-05 9.207412e-05 5.981788e-05 1.556188e-05 0
+#> PCr sIns Tau tNAA tCr tCho
+#> 1 2.101301e-05 6.508622e-06 0 7.537976e-05 6.121602e-05 1.603287e-05
#> Glx tLM09 tLM13 tLM20 X.CrCH2.sd Ala.sd
-#> 1 6.802629e-05 3.351727e-05 3.518179e-05 9.207422e-05 2.383752e-06 4.353323e-06
-#> Asp.sd Cr.sd GABA.sd Glc.sd Gln.sd GSH.sd
-#> 1 9.243631e-06 3.715171e-06 4.580083e-06 4.427049e-06 5.089146e-06 2.022838e-06
+#> 1 6.802609e-05 3.351727e-05 3.518176e-05 9.207412e-05 2.383751e-06 4.353321e-06
+#> Asp.sd Cr.sd GABA.sd Glc.sd Gln.sd GSH.sd
+#> 1 9.243624e-06 3.71518e-06 4.580067e-06 4.427043e-06 5.089142e-06 2.022836e-06
#> Glu.sd GPC.sd Ins.sd Lac.sd Lip09.sd Lip13a.sd
-#> 1 5.086891e-06 2.525936e-06 2.091042e-06 5.311859e-06 4.118788e-06 1.328562e-05
-#> Lip13b.sd Lip20.sd MM09.sd MM12.sd MM14.sd MM17.sd
-#> 1 6.477214e-06 7.510919e-06 3.827223e-06 4.597894e-06 7.234491e-06 3.810269e-06
-#> MM20.sd NAA.sd NAAG.sd PCh.sd PCr.sd sIns.sd
-#> 1 8.602468e-06 1.015226e-06 1.215671e-06 2.174696e-06 3.108033e-06 7.23386e-07
-#> Tau.sd tNAA.sd tCr.sd tCho.sd Glx.sd tLM09.sd
-#> 1 3.777987e-06 7.03106e-07 5.881707e-07 2.113501e-07 3.165047e-06 1.006533e-06
-#> tLM13.sd tLM20.sd phase lw shift asym
-#> 1 1.572003e-06 3.01819e-06 11.15085 5.038937 -0.003427611 0.1764494
+#> 1 5.086886e-06 2.525938e-06 2.091036e-06 5.311856e-06 4.118785e-06 1.328561e-05
+#> Lip13b.sd Lip20.sd MM09.sd MM12.sd MM14.sd MM17.sd
+#> 1 6.477209e-06 7.510914e-06 3.82722e-06 4.597893e-06 7.234487e-06 3.810266e-06
+#> MM20.sd NAA.sd NAAG.sd PCh.sd PCr.sd sIns.sd
+#> 1 8.602463e-06 1.015226e-06 1.215672e-06 2.1747e-06 3.108041e-06 7.233854e-07
+#> Tau.sd tNAA.sd tCr.sd tCho.sd Glx.sd tLM09.sd
+#> 1 3.777982e-06 7.031058e-07 5.881706e-07 2.113499e-07 3.165044e-06 1.006532e-06
+#> tLM13.sd tLM20.sd phase lw shift asym
+#> 1 1.572002e-06 3.018188e-06 11.1509 5.038938 -0.003427613 0.1764499
#> res.deviance res.niter res.info
-#> 1 7.300326e-05 28 2
+#> 1 7.300313e-05 28 2
#> res.message bl_ed_pppm
#> 1 Relative error between `par' and the solution is at most `ptol'. 2.364083
#> max_bl_flex_used full_res fit_pts ppm_range SNR SRR FQN
-#> 1 FALSE 7.745309e-05 497 3.8 62.79191 51.44065 1.490028
-#> tNAA_lw tCr_lw tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
-#> 1 0.0456527 0.05199591 0.0543881 -8.904402 -8.947808
+#> 1 FALSE 7.745303e-05 497 3.8 62.79191 51.44069 1.490026
+#> tNAA_lw tCr_lw tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
+#> 1 0.04565271 0.05199592 0.05438806 -8.904402 -8.947808
#> auto_bl_crit_4.942 auto_bl_crit_4.12 auto_bl_crit_3.425 auto_bl_crit_2.844
-#> 1 -8.980941 -9.003463 -9.016574 -9.023968
+#> 1 -8.980941 -9.003463 -9.016574 -9.023969
#> auto_bl_crit_2.364 auto_bl_crit_1.969 auto_bl_crit_1.647 auto_bl_crit_1.384
-#> 1 -9.027876 -9.027565 -9.014311 -8.963288
+#> 1 -9.027877 -9.027566 -9.014311 -8.963287
#> auto_bl_crit_1.17 auto_bl_crit_0.997 auto_bl_crit_0.856 auto_bl_crit_0.743
-#> 1 -8.848749 -8.694789 -8.565997 -8.488422
+#> 1 -8.848745 -8.694781 -8.565987 -8.48841
#> auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54
-#> 1 -8.449881 -8.432821 -8.425656 -8.422668
+#> 1 -8.449867 -8.432807 -8.425641 -8.422654
#> auto_bl_crit_0.532 auto_bl_crit_0.529
-#> 1 -8.421414 -8.420883
Note that signal names appended with “.sd” are the CRLB estimates for the uncertainty (standard deviation) in the metabolite quantity estimate. e.g. to calculate the percentage s.d. for tNAA:
fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100
-#> [1] 0.9327524
Spectral SNR:
fit_res$res_tab$SNR
@@ -249,7 +249,7 @@ Basis simulationLinewidth of the tNAA resonance in PPM:
fit_res$res_tab$tNAA_lw
-#> [1] 0.0456527
+#> [1] 0.04565271
An alternative method scales the metabolite values into molar (mM) units (mol / Litre of tissue) based on assumptions outlined in the LCModel manual and references therein (section 10.2). This approach may @@ -326,7 +326,7 @@
fit_res_molar <- scale_amp_molar(fit_res, mrs_data_wref)
fit_res_molar$res_tab$tNAA
-#> [1] 6.81759
Note, while “absolute” units are attractive, a large number of assumptions about metabolite and water relaxation rates are necessary to arrive at these mM estimates. If you’re not confident at being able to diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png index 454fbf49..57ac06c9 100644 Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png index 8131c46d..8ca44b0f 100644 Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/docs/articles/spant-metabolite-simulation.html b/docs/articles/spant-metabolite-simulation.html index 3fac9c0b..f212bcb6 100644 --- a/docs/articles/spant-metabolite-simulation.html +++ b/docs/articles/spant-metabolite-simulation.html @@ -40,7 +40,7 @@
diff --git a/docs/articles/spant-preprocessing.html b/docs/articles/spant-preprocessing.html index 8c244323..79d869eb 100644 --- a/docs/articles/spant-preprocessing.html +++ b/docs/articles/spant-preprocessing.html @@ -40,7 +40,7 @@ diff --git a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png index d59495c2..d418b8f4 100644 Binary files a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png index c97dee24..89993f67 100644 Binary files a/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png and b/docs/articles/spant-preprocessing_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/docs/authors.html b/docs/authors.html index 6defe087..3b935adf 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ diff --git a/docs/index.html b/docs/index.html index 92a76982..b6fc12b8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ diff --git a/docs/news/index.html b/docs/news/index.html index 59504b39..6428c301 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ @@ -73,7 +73,13 @@R/utils.R
+ find_mrs_files.Rd
Find valid MRS data files recursively from a directory path.
+find_mrs_files(dir)
a directory path.
a vector of valid MRS data files.
+fd_gauss_smo()
Apply a Gaussian smoother in the spectral domain.
Find valid MRS data files recursively from a directory path.