From 2c8dda4708002ced141a374854d824ef4741be2e Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 24 Aug 2022 16:20:55 +0200
Subject: [PATCH 01/46] Adapt to changes in rsfmri and suggestions for
 processing.

---
 R/rs_pipeline.R | 119 ++++++++++++++++++++++++++++++------------------
 1 file changed, 74 insertions(+), 45 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index a5ec461..b7180ff 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -2,7 +2,6 @@
 #'
 #' @param functional Path to a functional dataset.
 #' @param anatomy Path to a corresponing anatomical dataset.
-#' @param physfile Path to corresponding pyhsiological data.
 #' @param std_anat Path to standard anatomical file.
 #' @param std_white_matter Path to standard white matter mask.
 #' @param std_csf Path to standard CSF mask.
@@ -17,20 +16,31 @@
 rs_pipeline <- function(
         functional,
         anatomy,
-        physfile = NULL,
         std_anat,
         std_white_matter,
         std_csf,
         labels_img,
         labels_text,
+        magnitude_map,
+        phase_map,
+        dwell_time,
+        echo_spacing,
+        fnirt_conf,
         gsr = TRUE,
         tr = NULL,
         odd = NULL) {
+    old_scipen <- options(scipen = 200)
+    on.exit(options(old_scipen))
+
     std_anat <- normalizePath(std_anat)
+    std_brain <- normalizePath(std_brain)
+    std_hires <- normalizePath(std_hires)
     std_white_matter <- normalizePath(std_white_matter)
     std_csf <- normalizePath(std_csf)
     labels_img <- normalizePath(labels_img)
     labels_text <- normalizePath(labels_text)
+    mag_path <- normalizePath(magnitude_map)
+    pha_path <- normalizePath(phase_map)
 
     if (!is.null(physfile)) {
         input_files <- normalizePath(c(functional, anatomy, physfile))
@@ -39,54 +49,82 @@ rs_pipeline <- function(
     }
     input_dir <- dirname(functional)
 
-    print("Standardising orientation...")
-    ori_func <- rsfmri::fsl_reorient2std(input_files[1])
-    ori_anat <- rsfmri::fsl_reorient2std(input_files[2])
+    print_msg <- function(txt) {
+        print(paste(date(), txt))
+    }
+
+    print_msg("Standardising orientation...")
+    ori_func <- rsfmri::fsl_reorient2std(functional)
+    ori_anat <- rsfmri::fsl_reorient2std(anatomy)
 
-    print("Skull stripping...")
+    print_msg("Skull stripping...")
     skull_stripped <- rsfmri::skull_stripping(ori_func, anatomy = ori_anat)
 
-    print("Co-registering functional to standard...")
-    normalise <- rsfmri::register_functonal_to_standard(
-        skull_stripped[1], anatfile = skull_stripped[2],
-        standard = std_anat)
+    print_msg("Correcting motion...")
+    motion_cor <- rsfmri::fsl_mcflirt(ori_func)
+    motion_file <- paste0(motion_cor, ".par")
 
-    print("Extracting WM and CSF time course...")
-    wm_timecourse <- rsfmri::fsl_meants(normalise[1],
+    motion_check <- check_motion(parfile = motion_file, cutoff = 1,
+                                 plot = FALSE)
+    to_remove <- c(1:3, motion_check$flag_motion, motion_check$flag_spike)
+
+    if (motion_check$exceeds_motion > 3 ||
+        motion_check$exceeds_spike > min(c(20, nrow(rs_filtered) * 0.05))) {
+        stop("Excessive motion.")
+    }
+
+    print_msg("Segmentation...")
+    pve_wm <- rsfmri::fsl_fast(skull_stripped[2], smooth_extent = 10)
+    binary_wm <- rsfmri::fsl_maths_binary_segmentation(pve_wm)
+
+    print_msg("Generating Field Map...")
+    fm <- rsfmri::fsl_make_fieldmap(mag_path, pha_path, echo_spacing)
+
+    print_msg("EPI B0 Field Map Correction...")
+    epi_reg <- rsfmri::fsl_epi_reg(
+        motion_cor,
+        anatomical = ori_anat,
+        anatomical_brain = skull_stripped[2],
+        anatomical_wm_seg = binary_wm,
+        fmap = fm$fmap,
+        magnitude_map = fm$mag_norm,
+        magnitude_brain = fm$mag ,
+        pedir = "-y",
+        dwell_time = dwell_time
+    )
+
+    print_msg("Co-registering functional to standard...")
+    reg <- rsfmri::register_functonal_to_standard(
+        functional = motion_cor, bbr_warp = epi_reg, anatfile = ori_anat,
+        anat_extracted = skull_stripped[2], standard = std_anat,
+        standard_extracted = std_brain, standard_hires = std_hires,
+        fnirt_config = fnirt_conf)
+
+    print_msg("Extracting WM and CSF time course...")
+    wm_timecourse <- rsfmri::fsl_meants(reg,
                         outfile = file.path(input_dir, "wmtc.txt"),
                         maskfile = std_white_matter)
-    csf_timecourse <- rsfmri::fsl_meants(normalise[1],
+    csf_timecourse <- rsfmri::fsl_meants(reg,
                         outfile = file.path(input_dir, "csftc.txt"),
                         maskfile = std_csf)
     if (gsr) {
-        gs_timecourse <- rsfmri::fsl_meants(normalise[1],
+        gs_timecourse <- rsfmri::fsl_meants(motion_cor,
                 outfile = file.path(input_dir, "gs.txt"),
                 maskfile = file.path(input_dir, "mean_mask.nii.gz"))
     }
 
-    if (!is.null(physfile) && !is.null(tr)) {
-        print("Generating physiological confounds...")
-        tr_s <- tr / 1000
-        # need to sort out the other options to be more generalisable
-        physio_confounds <- rsfmri::fsl_pnm(
-            input_files[3], normalise[1], tr = tr_s)
-        physio_confounds <- file.path(input_dir, physio_confounds)
-    }
 
-    print("Correcting motion...")
-    motion_cor <- rsfmri::fsl_mcflirt(normalise[1])
 
     if (!is.null(tr) && !is.null(odd)) {
-        print("Correcting slice scan time...")
+        print_msg("Correcting slice scan time...")
         slice_timed <- rsfmri::fsl_slicetimer(
-            motion_cor[1], tr = as.character(tr), odd = odd)
+            reg, tr = as.character(tr), odd = odd)
     } else {
         # TODO: Make these a list or so, so we can check the last element.
-        slice_timed <- motion_cor
+        slice_timed <- reg
     }
 
     # Build file containing noise to "regress out".
-    motion_file <- paste0(motion_cor, ".par")
     if (gsr) {
         noise <- noise_file(motion_file, wm_timecourse, csf_timecourse,
                             gs_timecourse)
@@ -103,18 +141,17 @@ rs_pipeline <- function(
                        row.names = FALSE, col.names = FALSE)
 
     # call glm to get rid of all the noise
-    print("Removing noise...")
+    print_msg("Removing noise...")
     if (!is.null(physfile)) {
-        glm_out <- rsfmri::fsl_glm(slice_timed[1], outtype = "both",
+        glm_out <- rsfmri::fsl_glm(reg, outtype = "both",
                                    predictors = noise_file, demean = TRUE,
                                    physio_list = physio_confounds)
     } else {
-        glm_out <- rsfmri::fsl_glm(slice_timed[1], outtype = "both",
+        glm_out <- rsfmri::fsl_glm(reg, outtype = "both",
                            predictors = noise_file, demean = TRUE)
     }
-    print("Extracting AALv4 time courses")
+    print_msg("Extracting region time courses")
     labels <- rsfmri::fsl_meants(glm_out[1], label = labels_img)
-    print(labels[1])
 
     rs_tc <- readr::read_table2(labels[1], col_names = FALSE)
     rs_tc <- rs_tc[, apply(rs_tc, 2, function(x) !(all(is.na(x))))]
@@ -123,7 +160,7 @@ rs_pipeline <- function(
                                col_names = c("no", "name"), skip = 1)
     colnames(rs_tc) <- info[["name"]]
 
-    print("Filtering...")
+    print_msg("Filtering...")
     bandpass <- signal::butter(2, c(0.01, 0.15), "pass")
 
     rs_filtered <- scale(apply(
@@ -132,15 +169,7 @@ rs_pipeline <- function(
 
     rs_filtered <- tibble::as_tibble(rs_filtered)
 
-    print("Scrub time series...")
-    motion_check <- check_motion(parfile = motion_file, cutoff = 1,
-                                 plot = FALSE)
-    to_remove <- c(1:3, motion_check$flag_motion, motion_check$flag_spike)
-
-    if (motion_check$exceeds_motion > 3 ||
-        motion_check$exceeds_spike > min(c(20, nrow(rs_filtered) * 0.05))) {
-            stop("Excessive motion.")
-    }
+    print_msg("Scrub time series...")
     rs_filtered <- rs_filtered[-to_remove, ]
 
     rs_list <- list()
@@ -150,13 +179,13 @@ rs_pipeline <- function(
     x2sym <- rlang::sym("x2")
     corsym <- rlang::sym("cor")
 
-    print("Correlating")
+    print_msg("Correlating")
     rs_cor <- stats::cor(rs_filtered)
     rs_cor <- tibble::as_tibble(rs_cor, rownames = "x1") %>%
         tidyr::gather(!!x2sym, !!corsym, -!!x1sym)
 
     rs_list$correlation <- rs_cor
 
-    print("Done.")
+    print_msg("Done.")
     rs_list
 }
-- 
GitLab


From 3f6ccaa1120d6c4bf0cb82514d1904737d51cf12 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 25 Aug 2022 14:05:44 +0200
Subject: [PATCH 02/46] Update pipeline.

---
 R/rs_pipeline.R | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index b7180ff..7712840 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -76,6 +76,7 @@ rs_pipeline <- function(
     print_msg("Segmentation...")
     pve_wm <- rsfmri::fsl_fast(skull_stripped[2], smooth_extent = 10)
     binary_wm <- rsfmri::fsl_maths_binary_segmentation(pve_wm)
+    pve_basename <- gsub("_\\d.nii.gz$", "", pve_wm)
 
     print_msg("Generating Field Map...")
     fm <- rsfmri::fsl_make_fieldmap(mag_path, pha_path, echo_spacing)
@@ -101,20 +102,17 @@ rs_pipeline <- function(
         fnirt_config = fnirt_conf)
 
     print_msg("Extracting WM and CSF time course...")
-    wm_timecourse <- rsfmri::fsl_meants(reg,
-                        outfile = file.path(input_dir, "wmtc.txt"),
-                        maskfile = std_white_matter)
-    csf_timecourse <- rsfmri::fsl_meants(reg,
-                        outfile = file.path(input_dir, "csftc.txt"),
-                        maskfile = std_csf)
+    timecourses <- rsfmri::extract_csf_and_wm(
+        reg, pve_basename = pve_wm, std_brain = std_anat,
+        anat_to_mni_warp = file.path(input_dir, "t1_to_mni_warp.nii.gz")
+    )
+
     if (gsr) {
         gs_timecourse <- rsfmri::fsl_meants(motion_cor,
                 outfile = file.path(input_dir, "gs.txt"),
                 maskfile = file.path(input_dir, "mean_mask.nii.gz"))
     }
 
-
-
     if (!is.null(tr) && !is.null(odd)) {
         print_msg("Correcting slice scan time...")
         slice_timed <- rsfmri::fsl_slicetimer(
@@ -126,7 +124,7 @@ rs_pipeline <- function(
 
     # Build file containing noise to "regress out".
     if (gsr) {
-        noise <- noise_file(motion_file, wm_timecourse, csf_timecourse,
+        noise <- noise_file(motion_file, timecourses[1], timecourses[2],
                             gs_timecourse)
 
     } else {
-- 
GitLab


From 8bc6d97b122dbad65965b7b486e2fac53f0d8534 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 25 Aug 2022 14:25:41 +0200
Subject: [PATCH 03/46] Fix args & paths.

---
 R/rs_pipeline.R | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 7712840..3702a93 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -17,8 +17,7 @@ rs_pipeline <- function(
         functional,
         anatomy,
         std_anat,
-        std_white_matter,
-        std_csf,
+        std_brain,
         labels_img,
         labels_text,
         magnitude_map,
@@ -32,11 +31,10 @@ rs_pipeline <- function(
     old_scipen <- options(scipen = 200)
     on.exit(options(old_scipen))
 
+    functional <- normalizePath(functional)
+    anatomy <- normalizePath(anatomy)
     std_anat <- normalizePath(std_anat)
     std_brain <- normalizePath(std_brain)
-    std_hires <- normalizePath(std_hires)
-    std_white_matter <- normalizePath(std_white_matter)
-    std_csf <- normalizePath(std_csf)
     labels_img <- normalizePath(labels_img)
     labels_text <- normalizePath(labels_text)
     mag_path <- normalizePath(magnitude_map)
-- 
GitLab


From 78de84fe5dcbfcb31864a2bc991310a48f9c80d4 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 25 Aug 2022 14:28:01 +0200
Subject: [PATCH 04/46] Remove rests of physfile.

---
 R/rs_pipeline.R | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 3702a93..d83f1cd 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -40,11 +40,8 @@ rs_pipeline <- function(
     mag_path <- normalizePath(magnitude_map)
     pha_path <- normalizePath(phase_map)
 
-    if (!is.null(physfile)) {
-        input_files <- normalizePath(c(functional, anatomy, physfile))
-    } else {
-        input_files <- normalizePath(c(functional, anatomy))
-    }
+
+    input_files <- normalizePath(c(functional, anatomy))
     input_dir <- dirname(functional)
 
     print_msg <- function(txt) {
@@ -138,14 +135,9 @@ rs_pipeline <- function(
 
     # call glm to get rid of all the noise
     print_msg("Removing noise...")
-    if (!is.null(physfile)) {
-        glm_out <- rsfmri::fsl_glm(reg, outtype = "both",
-                                   predictors = noise_file, demean = TRUE,
-                                   physio_list = physio_confounds)
-    } else {
-        glm_out <- rsfmri::fsl_glm(reg, outtype = "both",
-                           predictors = noise_file, demean = TRUE)
-    }
+    glm_out <- rsfmri::fsl_glm(reg, outtype = "both",
+                       predictors = noise_file, demean = TRUE)
+
     print_msg("Extracting region time courses")
     labels <- rsfmri::fsl_meants(glm_out[1], label = labels_img)
 
-- 
GitLab


From b6882e9a8dd5d975293c744da75d405549b48503 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 25 Aug 2022 14:38:50 +0200
Subject: [PATCH 05/46] Refer to correct object.

---
 R/rs_pipeline.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index d83f1cd..49e5588 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -64,7 +64,7 @@ rs_pipeline <- function(
     to_remove <- c(1:3, motion_check$flag_motion, motion_check$flag_spike)
 
     if (motion_check$exceeds_motion > 3 ||
-        motion_check$exceeds_spike > min(c(20, nrow(rs_filtered) * 0.05))) {
+        motion_check$exceeds_spike > min(c(20, nrow(motion_check$data) * 0.05))) {
         stop("Excessive motion.")
     }
 
-- 
GitLab


From 8f4fad2f33d9fefe627086903ac3e2874a1d57a3 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 25 Aug 2022 16:03:44 +0200
Subject: [PATCH 06/46] Remove unnused arg.

---
 R/rs_pipeline.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 49e5588..12bc15a 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -93,7 +93,7 @@ rs_pipeline <- function(
     reg <- rsfmri::register_functonal_to_standard(
         functional = motion_cor, bbr_warp = epi_reg, anatfile = ori_anat,
         anat_extracted = skull_stripped[2], standard = std_anat,
-        standard_extracted = std_brain, standard_hires = std_hires,
+        standard_extracted = std_brain,
         fnirt_config = fnirt_conf)
 
     print_msg("Extracting WM and CSF time course...")
-- 
GitLab


From 28490c80d29849228505eb0fa405fcb317ccffff Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Fri, 26 Aug 2022 07:28:52 +0200
Subject: [PATCH 07/46] Fix noise file building,

---
 R/rs_pipeline.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 12bc15a..f1a7dd8 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -120,10 +120,11 @@ rs_pipeline <- function(
     # Build file containing noise to "regress out".
     if (gsr) {
         noise <- noise_file(motion_file, timecourses[1], timecourses[2],
-                            gs_timecourse)
+                            gs_timecourse, first_deriv = TRUE,
+                            second_deriv = TRUE, square = FALSE)
 
     } else {
-        noise <- noise_file(motion_file, wm_timecourse, csf_timecourse,
+        noise <- noise_file(motion_file, timecourses[1], timecourses[2],
                             first_deriv = TRUE, second_deriv = TRUE,
                             square = FALSE)
     }
-- 
GitLab


From 70fff4c106aee61f2d6cb62cb4409f2c01445fbf Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Fri, 26 Aug 2022 07:31:56 +0200
Subject: [PATCH 08/46] Fix PVE name.

---
 R/rs_pipeline.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index f1a7dd8..c9121ba 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -97,8 +97,9 @@ rs_pipeline <- function(
         fnirt_config = fnirt_conf)
 
     print_msg("Extracting WM and CSF time course...")
+    pve_use <- gsub("_\\d.nii.gz$", "", pve_wm)
     timecourses <- rsfmri::extract_csf_and_wm(
-        reg, pve_basename = pve_wm, std_brain = std_anat,
+        reg, pve_basename = pve_use, std_brain = std_anat,
         anat_to_mni_warp = file.path(input_dir, "t1_to_mni_warp.nii.gz")
     )
 
-- 
GitLab


From 5e515321c862119a0edc47a633c47b3b8ecb9e15 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Fri, 26 Aug 2022 08:40:12 +0200
Subject: [PATCH 09/46] Fix handling of column names.

---
 R/rs_pipeline.R | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index c9121ba..70e2d02 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -146,9 +146,11 @@ rs_pipeline <- function(
     rs_tc <- readr::read_table2(labels[1], col_names = FALSE)
     rs_tc <- rs_tc[, apply(rs_tc, 2, function(x) !(all(is.na(x))))]
 
-    info <- readr::read_table(labels_text,
-                               col_names = c("no", "name"), skip = 1)
-    colnames(rs_tc) <- info[["name"]]
+    info <- readr::read_table(labels_text, col_names = c("no", "name"))
+    colnames(rs_tc)[info$no] <- info$name
+    null_cols <- apply(rs_tc, 2, function(x) all(x == 0))
+    rs_tc[null_cols] <- NULL
+
 
     print_msg("Filtering...")
     bandpass <- signal::butter(2, c(0.01, 0.15), "pass")
-- 
GitLab


From 98470f7ac838d8e7ba3eab1749dc398e7c039799 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Fri, 26 Aug 2022 13:00:17 +0200
Subject: [PATCH 10/46] Update pipeline.

* Fix docs.
* Make it tidy up after itself.
---
 R/rs_pipeline.R    | 67 +++++++++++++++++++++++++++++++---------------
 man/rs_pipeline.Rd | 27 ++++++++++++-------
 2 files changed, 63 insertions(+), 31 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 70e2d02..f498aa8 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -1,12 +1,16 @@
 #' Run a complete resting-state fMRI pipeline.
 #'
 #' @param functional Path to a functional dataset.
-#' @param anatomy Path to a corresponing anatomical dataset.
+#' @param anatomy Path to a corresponding anatomical dataset.
 #' @param std_anat Path to standard anatomical file.
-#' @param std_white_matter Path to standard white matter mask.
-#' @param std_csf Path to standard CSF mask.
+#' @param std_brain Path to skull stripped standard file.
 #' @param labels_img Path to atlas image.
 #' @param labels_text Path to atlas label info file.
+#' @param magnitude_map Path to magnitude B0 map.
+#' @param phase_map Path to phase B0 map.
+#' @param dwell_time Dwell time in s.
+#' @param echo_spacing Echo spacing time in ms.
+#' @param fnirt_conf Name of the FSL fnirt config file to use.
 #' @param gsr Boolean whether to use global signal regression.
 #' @param tr The TR of the data im ms.
 #' @param odd Bool indicating whether slices were acquired interleaved.
@@ -32,17 +36,31 @@ rs_pipeline <- function(
     on.exit(options(old_scipen))
 
     functional <- normalizePath(functional)
-    anatomy <- normalizePath(anatomy)
+    input_dir <- dirname(functional)
+    temp_name <- paste0("proc", as.numeric(Sys.time()))
+    temp_dir <- file.path(input_dir, temp_name)
+    dir.create(temp_dir)
+
+    copy_to_temp <- function(in_file, temp_dir) {
+        old_path <- normalizePath(in_file)
+        base <- basename(in_file)
+        new <- file.path(temp_dir, base)
+        copy_success <- file.copy(old_path, new)
+        if (!copy_success) {
+            stop("could not copy")
+        }
+        new
+    }
+
+    functional <- copy_to_temp(functional, temp_dir)
+    anatomy <- copy_to_temp(anatomy, temp_dir)
+    mag_path <- copy_to_temp(magnitude_map, temp_dir)
+    pha_path <- copy_to_temp(phase_map, temp_dir)
+
     std_anat <- normalizePath(std_anat)
     std_brain <- normalizePath(std_brain)
     labels_img <- normalizePath(labels_img)
     labels_text <- normalizePath(labels_text)
-    mag_path <- normalizePath(magnitude_map)
-    pha_path <- normalizePath(phase_map)
-
-
-    input_files <- normalizePath(c(functional, anatomy))
-    input_dir <- dirname(functional)
 
     print_msg <- function(txt) {
         print(paste(date(), txt))
@@ -64,14 +82,14 @@ rs_pipeline <- function(
     to_remove <- c(1:3, motion_check$flag_motion, motion_check$flag_spike)
 
     if (motion_check$exceeds_motion > 3 ||
-        motion_check$exceeds_spike > min(c(20, nrow(motion_check$data) * 0.05))) {
+        motion_check$exceeds_spike > min(
+            c(20, nrow(motion_check$data) * 0.05))) {
         stop("Excessive motion.")
     }
 
     print_msg("Segmentation...")
     pve_wm <- rsfmri::fsl_fast(skull_stripped[2], smooth_extent = 10)
     binary_wm <- rsfmri::fsl_maths_binary_segmentation(pve_wm)
-    pve_basename <- gsub("_\\d.nii.gz$", "", pve_wm)
 
     print_msg("Generating Field Map...")
     fm <- rsfmri::fsl_make_fieldmap(mag_path, pha_path, echo_spacing)
@@ -84,7 +102,7 @@ rs_pipeline <- function(
         anatomical_wm_seg = binary_wm,
         fmap = fm$fmap,
         magnitude_map = fm$mag_norm,
-        magnitude_brain = fm$mag ,
+        magnitude_brain = fm$mag,
         pedir = "-y",
         dwell_time = dwell_time
     )
@@ -100,13 +118,13 @@ rs_pipeline <- function(
     pve_use <- gsub("_\\d.nii.gz$", "", pve_wm)
     timecourses <- rsfmri::extract_csf_and_wm(
         reg, pve_basename = pve_use, std_brain = std_anat,
-        anat_to_mni_warp = file.path(input_dir, "t1_to_mni_warp.nii.gz")
+        anat_to_mni_warp = file.path(temp_dir, "t1_to_mni_warp.nii.gz")
     )
 
     if (gsr) {
         gs_timecourse <- rsfmri::fsl_meants(motion_cor,
-                outfile = file.path(input_dir, "gs.txt"),
-                maskfile = file.path(input_dir, "mean_mask.nii.gz"))
+                outfile = file.path(temp_dir, "gs.txt"),
+                maskfile = file.path(temp_dir, "mean_mask.nii.gz"))
     }
 
     if (!is.null(tr) && !is.null(odd)) {
@@ -131,14 +149,14 @@ rs_pipeline <- function(
     }
     noise <- tibble::as_tibble(noise)
 
-    noise_file <- file.path(input_dir, "noise.txt")
-    utils::write.table(noise, file = file.path(input_dir, "noise.txt"),
+    noise_file <- file.path(temp_dir, "noise.txt")
+    utils::write.table(noise, file = file.path(temp_dir, "noise.txt"),
                        row.names = FALSE, col.names = FALSE)
 
     # call glm to get rid of all the noise
     print_msg("Removing noise...")
-    glm_out <- rsfmri::fsl_glm(reg, outtype = "both",
-                       predictors = noise_file, demean = TRUE)
+    glm_out <- rsfmri::fsl_glm(slice_timed, outtype = "both",
+                               predictors = noise_file, demean = TRUE)
 
     print_msg("Extracting region time courses")
     labels <- rsfmri::fsl_meants(glm_out[1], label = labels_img)
@@ -151,7 +169,6 @@ rs_pipeline <- function(
     null_cols <- apply(rs_tc, 2, function(x) all(x == 0))
     rs_tc[null_cols] <- NULL
 
-
     print_msg("Filtering...")
     bandpass <- signal::butter(2, c(0.01, 0.15), "pass")
 
@@ -171,13 +188,19 @@ rs_pipeline <- function(
     x2sym <- rlang::sym("x2")
     corsym <- rlang::sym("cor")
 
-    print_msg("Correlating")
+    print_msg("Correlating...")
     rs_cor <- stats::cor(rs_filtered)
     rs_cor <- tibble::as_tibble(rs_cor, rownames = "x1") %>%
         tidyr::gather(!!x2sym, !!corsym, -!!x1sym)
 
     rs_list$correlation <- rs_cor
 
+    print_msg("Tidying up...")
+    file.copy(rs_tc, input_dir)
+    file.copy(glm_out[1], input_dir)
+    file.copy(motion_file, input_dir)
+    unlink(temp_dir, recursive = TRUE)
+
     print_msg("Done.")
     rs_list
 }
diff --git a/man/rs_pipeline.Rd b/man/rs_pipeline.Rd
index 96d7ce9..ef09cd7 100644
--- a/man/rs_pipeline.Rd
+++ b/man/rs_pipeline.Rd
@@ -7,12 +7,15 @@
 rs_pipeline(
   functional,
   anatomy,
-  physfile = NULL,
   std_anat,
-  std_white_matter,
-  std_csf,
+  std_brain,
   labels_img,
   labels_text,
+  magnitude_map,
+  phase_map,
+  dwell_time,
+  echo_spacing,
+  fnirt_conf,
   gsr = TRUE,
   tr = NULL,
   odd = NULL
@@ -21,20 +24,26 @@ rs_pipeline(
 \arguments{
 \item{functional}{Path to a functional dataset.}
 
-\item{anatomy}{Path to a corresponing anatomical dataset.}
-
-\item{physfile}{Path to corresponding pyhsiological data.}
+\item{anatomy}{Path to a corresponding anatomical dataset.}
 
 \item{std_anat}{Path to standard anatomical file.}
 
-\item{std_white_matter}{Path to standard white matter mask.}
-
-\item{std_csf}{Path to standard CSF mask.}
+\item{std_brain}{Path to skull stripped standard file.}
 
 \item{labels_img}{Path to atlas image.}
 
 \item{labels_text}{Path to atlas label info file.}
 
+\item{magnitude_map}{Path to magnitude B0 map.}
+
+\item{phase_map}{Path to phase B0 map.}
+
+\item{dwell_time}{Dwell time in s.}
+
+\item{echo_spacing}{Echo spacing time in ms.}
+
+\item{fnirt_conf}{Name of the FSL fnirt config file to use.}
+
 \item{gsr}{Boolean whether to use global signal regression.}
 
 \item{tr}{The TR of the data im ms.}
-- 
GitLab


From a6206c1135e7b9c5a12290aa6c922095ab76dc55 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Fri, 26 Aug 2022 14:03:08 +0200
Subject: [PATCH 11/46] Fix copying.

---
 R/rs_pipeline.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index f498aa8..2d7ee57 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -196,7 +196,7 @@ rs_pipeline <- function(
     rs_list$correlation <- rs_cor
 
     print_msg("Tidying up...")
-    file.copy(rs_tc, input_dir)
+    file.copy(labels[1], input_dir)
     file.copy(glm_out[1], input_dir)
     file.copy(motion_file, input_dir)
     unlink(temp_dir, recursive = TRUE)
-- 
GitLab


From 5e5801461f6180c70d54eb6798a3847fba3fdf40 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 28 Sep 2022 12:44:58 +0200
Subject: [PATCH 12/46] Return more Bayesian statistics.

---
 R/compare_measure_group.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/compare_measure_group.R b/R/compare_measure_group.R
index 6fd54d6..4bb2b10 100644
--- a/R/compare_measure_group.R
+++ b/R/compare_measure_group.R
@@ -40,7 +40,7 @@ compare_measure_group <- function(rawlist, dv, ..., add_name = FALSE,
     dplyr::mutate(s.value = -log2(.data$p.value))
 
   bayes <- rstanarm::stan_glm(frml, data = grplist, iter = 2000, refresh = 0)
-  bayes_tbl <- parameters::parameters(bayes)
+  bayes_tbl <- parameters::parameters(bayes, test = "all")
 
   list(lm = mod, lm_tbl = modtbl,
        anova = av, anova_tbl = tbl,
-- 
GitLab


From 86f1e06d4c4f9de4d0f530f10f756ba4b32ac4d9 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 28 Sep 2022 12:45:30 +0200
Subject: [PATCH 13/46] Update pipeline, so...

* fieldmaps are optional
* intermediate files can be kept
---
 R/rs_pipeline.R | 90 +++++++++++++++++++++++++++++++------------------
 1 file changed, 58 insertions(+), 32 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 2d7ee57..e24226c 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -14,6 +14,8 @@
 #' @param gsr Boolean whether to use global signal regression.
 #' @param tr The TR of the data im ms.
 #' @param odd Bool indicating whether slices were acquired interleaved.
+#' @param keep_intermediate Should itermediate files be kept on disk? This is
+#' useful for debugging.
 #'
 #' @return A list containing time courses and a pairwise correlation matrix.
 #' @export
@@ -24,14 +26,15 @@ rs_pipeline <- function(
         std_brain,
         labels_img,
         labels_text,
-        magnitude_map,
-        phase_map,
-        dwell_time,
-        echo_spacing,
+        magnitude_map = NULL,
+        phase_map = NULL,
+        dwell_time = NULL,
+        echo_spacing = NULL,
         fnirt_conf,
         gsr = TRUE,
         tr = NULL,
-        odd = NULL) {
+        odd = NULL,
+        keep_intermediate = FALSE) {
     old_scipen <- options(scipen = 200)
     on.exit(options(old_scipen))
 
@@ -54,8 +57,11 @@ rs_pipeline <- function(
 
     functional <- copy_to_temp(functional, temp_dir)
     anatomy <- copy_to_temp(anatomy, temp_dir)
-    mag_path <- copy_to_temp(magnitude_map, temp_dir)
-    pha_path <- copy_to_temp(phase_map, temp_dir)
+
+    if (!is.null(magnitude_map) | !is.null(phase_map)) {
+        mag_path <- copy_to_temp(magnitude_map, temp_dir)
+        pha_path <- copy_to_temp(phase_map, temp_dir)
+    }
 
     std_anat <- normalizePath(std_anat)
     std_brain <- normalizePath(std_brain)
@@ -74,8 +80,9 @@ rs_pipeline <- function(
     skull_stripped <- rsfmri::skull_stripping(ori_func, anatomy = ori_anat)
 
     print_msg("Correcting motion...")
-    motion_cor <- rsfmri::fsl_mcflirt(ori_func)
-    motion_file <- paste0(motion_cor, ".par")
+    motion_cor <- rsfmri::fsl_mcflirt(ori_func, meanvol = TRUE)
+    mean_motion_reg <- gsub(".nii.gz", "_mean_reg.nii.gz", motion_cor)
+    motion_file <- gsub(".nii.gz", ".par", motion_cor)
 
     motion_check <- check_motion(parfile = motion_file, cutoff = 1,
                                  plot = FALSE)
@@ -91,28 +98,45 @@ rs_pipeline <- function(
     pve_wm <- rsfmri::fsl_fast(skull_stripped[2], smooth_extent = 10)
     binary_wm <- rsfmri::fsl_maths_binary_segmentation(pve_wm)
 
-    print_msg("Generating Field Map...")
-    fm <- rsfmri::fsl_make_fieldmap(mag_path, pha_path, echo_spacing)
-
-    print_msg("EPI B0 Field Map Correction...")
-    epi_reg <- rsfmri::fsl_epi_reg(
-        motion_cor,
-        anatomical = ori_anat,
-        anatomical_brain = skull_stripped[2],
-        anatomical_wm_seg = binary_wm,
-        fmap = fm$fmap,
-        magnitude_map = fm$mag_norm,
-        magnitude_brain = fm$mag,
-        pedir = "-y",
-        dwell_time = dwell_time
-    )
-
-    print_msg("Co-registering functional to standard...")
-    reg <- rsfmri::register_functonal_to_standard(
-        functional = motion_cor, bbr_warp = epi_reg, anatfile = ori_anat,
-        anat_extracted = skull_stripped[2], standard = std_anat,
-        standard_extracted = std_brain,
-        fnirt_config = fnirt_conf)
+    if (!is.null(magnitude_map) | !is.null(phase_map)) {
+        print_msg("Generating Field Map...")
+        fm <- rsfmri::fsl_make_fieldmap(mag_path, pha_path, echo_spacing)
+
+        print_msg("EPI B0 Field Map Correction...")
+        epi_reg <- rsfmri::fsl_epi_reg(
+            mean_motion_reg,
+            anatomical = ori_anat,
+            anatomical_brain = skull_stripped[2],
+            anatomical_wm_seg = binary_wm,
+            fmap = fm$fmap,
+            magnitude_map = fm$mag_norm,
+            magnitude_brain = fm$mag,
+            pedir = "-y",
+            dwell_time = dwell_time
+        )
+
+        print_msg("Co-registering functional to standard...")
+        reg <- rsfmri::register_functonal_to_standard(
+            functional = motion_cor, bbr_warp = epi_reg, anatfile = ori_anat,
+            anat_extracted = skull_stripped[2], standard = std_anat,
+            standard_extracted = std_brain,
+            fnirt_config = fnirt_conf)
+    } else {
+        print_msg("Co-registering functional to standard (1/2)...")
+        epi_reg <- rsfmri::fsl_epi_reg(
+            motion_cor,
+            anatomical = ori_anat,
+            anatomical_brain = skull_stripped[2],
+            anatomical_wm_seg = binary_wm
+        )
+
+        print_msg("Co-registering functional to standard (2/2)...")
+        reg <- rsfmri::register_functonal_to_standard(
+            functional = motion_cor, anatfile = ori_anat,
+            anat_extracted = skull_stripped[2], standard = std_anat,
+            standard_extracted = std_brain,
+            fnirt_config = fnirt_conf)
+    }
 
     print_msg("Extracting WM and CSF time course...")
     pve_use <- gsub("_\\d.nii.gz$", "", pve_wm)
@@ -199,7 +223,9 @@ rs_pipeline <- function(
     file.copy(labels[1], input_dir)
     file.copy(glm_out[1], input_dir)
     file.copy(motion_file, input_dir)
-    unlink(temp_dir, recursive = TRUE)
+    if (!keep_intermediate) {
+        unlink(temp_dir, recursive = TRUE)
+    }
 
     print_msg("Done.")
     rs_list
-- 
GitLab


From 2c0e701253712bf08b2f5f3eb2d27fc98245d4d5 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 28 Sep 2022 13:06:39 +0200
Subject: [PATCH 14/46] Try fixing parameters.

---
 R/compare_measure_group.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/compare_measure_group.R b/R/compare_measure_group.R
index 4bb2b10..19b89cf 100644
--- a/R/compare_measure_group.R
+++ b/R/compare_measure_group.R
@@ -40,7 +40,7 @@ compare_measure_group <- function(rawlist, dv, ..., add_name = FALSE,
     dplyr::mutate(s.value = -log2(.data$p.value))
 
   bayes <- rstanarm::stan_glm(frml, data = grplist, iter = 2000, refresh = 0)
-  bayes_tbl <- parameters::parameters(bayes, test = "all")
+  bayes_tbl <- parameters::model_parameters(bayes, test = "all")
 
   list(lm = mod, lm_tbl = modtbl,
        anova = av, anova_tbl = tbl,
-- 
GitLab


From 5a91bcb2116f9297c621098e880d7cd98e588641 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 28 Sep 2022 13:52:56 +0200
Subject: [PATCH 15/46] Fix params for real.

---
 R/compare_measure_group.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/compare_measure_group.R b/R/compare_measure_group.R
index 19b89cf..d3e1f66 100644
--- a/R/compare_measure_group.R
+++ b/R/compare_measure_group.R
@@ -40,7 +40,8 @@ compare_measure_group <- function(rawlist, dv, ..., add_name = FALSE,
     dplyr::mutate(s.value = -log2(.data$p.value))
 
   bayes <- rstanarm::stan_glm(frml, data = grplist, iter = 2000, refresh = 0)
-  bayes_tbl <- parameters::model_parameters(bayes, test = "all")
+  bayes_tbl <- parameters::model_parameters(bayes,
+                                            test = c("pd", "rope", "bf"))
 
   list(lm = mod, lm_tbl = modtbl,
        anova = av, anova_tbl = tbl,
-- 
GitLab


From 8d31c84947352a36509e537e1b1e5a3083c81b13 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Fri, 30 Sep 2022 10:56:40 +0200
Subject: [PATCH 16/46] Add scaling option to rspipeline.

---
 R/rs_pipeline.R    |  8 ++++++++
 man/rs_pipeline.Rd | 18 +++++++++++++-----
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index e24226c..6096c14 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -14,6 +14,8 @@
 #' @param gsr Boolean whether to use global signal regression.
 #' @param tr The TR of the data im ms.
 #' @param odd Bool indicating whether slices were acquired interleaved.
+#' @param scale_anat_to Optional value to scale the anatomical image resolution
+#' to.
 #' @param keep_intermediate Should itermediate files be kept on disk? This is
 #' useful for debugging.
 #'
@@ -34,6 +36,7 @@ rs_pipeline <- function(
         gsr = TRUE,
         tr = NULL,
         odd = NULL,
+        scale_anat_to = NULL,
         keep_intermediate = FALSE) {
     old_scipen <- options(scipen = 200)
     on.exit(options(old_scipen))
@@ -76,6 +79,11 @@ rs_pipeline <- function(
     ori_func <- rsfmri::fsl_reorient2std(functional)
     ori_anat <- rsfmri::fsl_reorient2std(anatomy)
 
+    if (!is.null(scale_anat_to)) {
+        print_msg("Rescaling anatomical data")
+        ori_anat <- rsfmri::rescale_image(ori_anat, res = 2)
+    }
+
     print_msg("Skull stripping...")
     skull_stripped <- rsfmri::skull_stripping(ori_func, anatomy = ori_anat)
 
diff --git a/man/rs_pipeline.Rd b/man/rs_pipeline.Rd
index ef09cd7..16d4258 100644
--- a/man/rs_pipeline.Rd
+++ b/man/rs_pipeline.Rd
@@ -11,14 +11,16 @@ rs_pipeline(
   std_brain,
   labels_img,
   labels_text,
-  magnitude_map,
-  phase_map,
-  dwell_time,
-  echo_spacing,
+  magnitude_map = NULL,
+  phase_map = NULL,
+  dwell_time = NULL,
+  echo_spacing = NULL,
   fnirt_conf,
   gsr = TRUE,
   tr = NULL,
-  odd = NULL
+  odd = NULL,
+  scale_anat_to = NULL,
+  keep_intermediate = FALSE
 )
 }
 \arguments{
@@ -49,6 +51,12 @@ rs_pipeline(
 \item{tr}{The TR of the data im ms.}
 
 \item{odd}{Bool indicating whether slices were acquired interleaved.}
+
+\item{scale_anat_to}{Optional value to scale the anatomical image resolution
+to.}
+
+\item{keep_intermediate}{Should itermediate files be kept on disk? This is
+useful for debugging.}
 }
 \value{
 A list containing time courses and a pairwise correlation matrix.
-- 
GitLab


From 359c9bcaa7aa01ca4429e315344dc5ab43102ded Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 12 Oct 2022 09:25:08 +0200
Subject: [PATCH 17/46] Fix pipeline.

---
 R/rs_pipeline.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 6096c14..fce0efc 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -140,7 +140,7 @@ rs_pipeline <- function(
 
         print_msg("Co-registering functional to standard (2/2)...")
         reg <- rsfmri::register_functonal_to_standard(
-            functional = motion_cor, anatfile = ori_anat,
+            functional = epi_reg, anatfile = ori_anat,
             anat_extracted = skull_stripped[2], standard = std_anat,
             standard_extracted = std_brain,
             fnirt_config = fnirt_conf)
-- 
GitLab


From 82a0db56297f1923280991aff326c04626559845 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Tue, 25 Oct 2022 14:08:50 +0200
Subject: [PATCH 18/46] Include AP/PA way of fieldmap generation.

---
 R/rs_pipeline.R | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index fce0efc..2ae1361 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -31,6 +31,9 @@ rs_pipeline <- function(
         magnitude_map = NULL,
         phase_map = NULL,
         dwell_time = NULL,
+        ap_map = NULL,
+        pa_map = NULL,
+        readout_time = NULL,
         echo_spacing = NULL,
         fnirt_conf,
         gsr = TRUE,
@@ -66,6 +69,11 @@ rs_pipeline <- function(
         pha_path <- copy_to_temp(phase_map, temp_dir)
     }
 
+    if (!is.null(ap_map) | !is.null(pa_map)) {
+        ap_path <- copy_to_temp(ap_map, temp_dir)
+        pa_path <- copy_to_temp(pa_path, temp_dir)
+    }
+
     std_anat <- normalizePath(std_anat)
     std_brain <- normalizePath(std_brain)
     labels_img <- normalizePath(labels_img)
@@ -106,9 +114,20 @@ rs_pipeline <- function(
     pve_wm <- rsfmri::fsl_fast(skull_stripped[2], smooth_extent = 10)
     binary_wm <- rsfmri::fsl_maths_binary_segmentation(pve_wm)
 
-    if (!is.null(magnitude_map) | !is.null(phase_map)) {
+    map_mag_pha <- all(c(!is.null(magnitude_map), !is.null(phase_map)))
+    map_ap_pa <- all(c(!is.null(ap_path), !is.null(pa_path)))
+
+    if (map_mag_pha & mag_ap_pa) {
+        stop("Either use Mag/Pha map or AP/PA, not both.")
+    }
+
+    if (mag_mag_pha | mag_ap_pa) {
         print_msg("Generating Field Map...")
-        fm <- rsfmri::fsl_make_fieldmap(mag_path, pha_path, echo_spacing)
+        if (mag_mag_pha) {
+            fm <- rsfmri::fsl_make_fieldmap(mag_path, pha_path, echo_spacing)
+        } else if (mag_ap_pa) {
+            fm <- rsfmri::fsl_make_fieldmap_pe(ap_map, pa_map, readout_time)
+        }
 
         print_msg("EPI B0 Field Map Correction...")
         epi_reg <- rsfmri::fsl_epi_reg(
-- 
GitLab


From dac8eb27140cc34685f7a70e1e106cd4782909a5 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Tue, 25 Oct 2022 15:44:48 +0200
Subject: [PATCH 19/46] fix

---
 R/rs_pipeline.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 2ae1361..35447b8 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -71,7 +71,7 @@ rs_pipeline <- function(
 
     if (!is.null(ap_map) | !is.null(pa_map)) {
         ap_path <- copy_to_temp(ap_map, temp_dir)
-        pa_path <- copy_to_temp(pa_path, temp_dir)
+        pa_path <- copy_to_temp(pa_map, temp_dir)
     }
 
     std_anat <- normalizePath(std_anat)
-- 
GitLab


From 69ad2f3ca1ee8adb393ab71faa5f3b3b3bb34eb4 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Tue, 25 Oct 2022 16:08:53 +0200
Subject: [PATCH 20/46] fix

---
 R/rs_pipeline.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 35447b8..cdf644c 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -117,15 +117,15 @@ rs_pipeline <- function(
     map_mag_pha <- all(c(!is.null(magnitude_map), !is.null(phase_map)))
     map_ap_pa <- all(c(!is.null(ap_path), !is.null(pa_path)))
 
-    if (map_mag_pha & mag_ap_pa) {
+    if (map_mag_pha & map_ap_pa) {
         stop("Either use Mag/Pha map or AP/PA, not both.")
     }
 
-    if (mag_mag_pha | mag_ap_pa) {
+    if (mag_mag_pha | map_ap_pa) {
         print_msg("Generating Field Map...")
         if (mag_mag_pha) {
             fm <- rsfmri::fsl_make_fieldmap(mag_path, pha_path, echo_spacing)
-        } else if (mag_ap_pa) {
+        } else if (map_ap_pa) {
             fm <- rsfmri::fsl_make_fieldmap_pe(ap_map, pa_map, readout_time)
         }
 
-- 
GitLab


From f53434464034d879cc0021cf9d5a9b48623b0fe4 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Tue, 25 Oct 2022 16:41:21 +0200
Subject: [PATCH 21/46] fix again

---
 R/rs_pipeline.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index cdf644c..414be56 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -121,9 +121,9 @@ rs_pipeline <- function(
         stop("Either use Mag/Pha map or AP/PA, not both.")
     }
 
-    if (mag_mag_pha | map_ap_pa) {
+    if (map_mag_pha | map_ap_pa) {
         print_msg("Generating Field Map...")
-        if (mag_mag_pha) {
+        if (map_mag_pha) {
             fm <- rsfmri::fsl_make_fieldmap(mag_path, pha_path, echo_spacing)
         } else if (map_ap_pa) {
             fm <- rsfmri::fsl_make_fieldmap_pe(ap_map, pa_map, readout_time)
-- 
GitLab


From 5e49bc255e1f7ad1979f596435e98ce8e1c0cd41 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 26 Oct 2022 08:14:49 +0200
Subject: [PATCH 22/46] Fix fieldmap generation.

---
 R/rs_pipeline.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 414be56..60df303 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -126,7 +126,7 @@ rs_pipeline <- function(
         if (map_mag_pha) {
             fm <- rsfmri::fsl_make_fieldmap(mag_path, pha_path, echo_spacing)
         } else if (map_ap_pa) {
-            fm <- rsfmri::fsl_make_fieldmap_pe(ap_map, pa_map, readout_time)
+            fm <- rsfmri::fsl_make_fieldmap_pe(ap_path, pa_path, readout_time)
         }
 
         print_msg("EPI B0 Field Map Correction...")
-- 
GitLab


From a9240d8457e4875a83da08f00d69d953ed63d66e Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Fri, 28 Oct 2022 13:07:09 +0200
Subject: [PATCH 23/46] Make motion cutoff an option.

---
 R/rs_pipeline.R    |  7 ++++++-
 man/rs_pipeline.Rd | 12 ++++++++++++
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 60df303..f35581c 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -9,6 +9,9 @@
 #' @param magnitude_map Path to magnitude B0 map.
 #' @param phase_map Path to phase B0 map.
 #' @param dwell_time Dwell time in s.
+#' @param ap_map Phase map in AP direction.
+#' @param pa_map Phase map in PA direction.
+#' @param readout_time Readout time for AP/PA fieldmaps.
 #' @param echo_spacing Echo spacing time in ms.
 #' @param fnirt_conf Name of the FSL fnirt config file to use.
 #' @param gsr Boolean whether to use global signal regression.
@@ -16,6 +19,7 @@
 #' @param odd Bool indicating whether slices were acquired interleaved.
 #' @param scale_anat_to Optional value to scale the anatomical image resolution
 #' to.
+#' @param motion_cutoff Motion correction cutoff value in deg/mm.
 #' @param keep_intermediate Should itermediate files be kept on disk? This is
 #' useful for debugging.
 #'
@@ -40,6 +44,7 @@ rs_pipeline <- function(
         tr = NULL,
         odd = NULL,
         scale_anat_to = NULL,
+        motion_cutoff = 1,
         keep_intermediate = FALSE) {
     old_scipen <- options(scipen = 200)
     on.exit(options(old_scipen))
@@ -100,7 +105,7 @@ rs_pipeline <- function(
     mean_motion_reg <- gsub(".nii.gz", "_mean_reg.nii.gz", motion_cor)
     motion_file <- gsub(".nii.gz", ".par", motion_cor)
 
-    motion_check <- check_motion(parfile = motion_file, cutoff = 1,
+    motion_check <- check_motion(parfile = motion_file, cutoff = motion_cutoff,
                                  plot = FALSE)
     to_remove <- c(1:3, motion_check$flag_motion, motion_check$flag_spike)
 
diff --git a/man/rs_pipeline.Rd b/man/rs_pipeline.Rd
index 16d4258..5d7de31 100644
--- a/man/rs_pipeline.Rd
+++ b/man/rs_pipeline.Rd
@@ -14,12 +14,16 @@ rs_pipeline(
   magnitude_map = NULL,
   phase_map = NULL,
   dwell_time = NULL,
+  ap_map = NULL,
+  pa_map = NULL,
+  readout_time = NULL,
   echo_spacing = NULL,
   fnirt_conf,
   gsr = TRUE,
   tr = NULL,
   odd = NULL,
   scale_anat_to = NULL,
+  motion_cutoff = 1,
   keep_intermediate = FALSE
 )
 }
@@ -42,6 +46,12 @@ rs_pipeline(
 
 \item{dwell_time}{Dwell time in s.}
 
+\item{ap_map}{Phase map in AP direction.}
+
+\item{pa_map}{Phase map in PA direction.}
+
+\item{readout_time}{Readout time for AP/PA fieldmaps.}
+
 \item{echo_spacing}{Echo spacing time in ms.}
 
 \item{fnirt_conf}{Name of the FSL fnirt config file to use.}
@@ -55,6 +65,8 @@ rs_pipeline(
 \item{scale_anat_to}{Optional value to scale the anatomical image resolution
 to.}
 
+\item{motion_cutoff}{Motion correction cutoff value in deg/mm.}
+
 \item{keep_intermediate}{Should itermediate files be kept on disk? This is
 useful for debugging.}
 }
-- 
GitLab


From 8ede9f227db240ec5f7ccaaedf5ab461a3a50615 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Fri, 28 Oct 2022 13:49:39 +0200
Subject: [PATCH 24/46] Add defaults for optional paths.

---
 R/rs_pipeline.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index f35581c..d4ea45d 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -69,11 +69,15 @@ rs_pipeline <- function(
     functional <- copy_to_temp(functional, temp_dir)
     anatomy <- copy_to_temp(anatomy, temp_dir)
 
+    mag_path <- NULL
+    pha_path <- NULL
     if (!is.null(magnitude_map) | !is.null(phase_map)) {
         mag_path <- copy_to_temp(magnitude_map, temp_dir)
         pha_path <- copy_to_temp(phase_map, temp_dir)
     }
 
+    ap_path <- NULL
+    pa_path <- NULL
     if (!is.null(ap_map) | !is.null(pa_map)) {
         ap_path <- copy_to_temp(ap_map, temp_dir)
         pa_path <- copy_to_temp(pa_map, temp_dir)
-- 
GitLab


From f6b8bdb4e679237fc0b380bb12542441a29d2a60 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 10 Nov 2022 16:50:06 +0100
Subject: [PATCH 25/46] Fix bug in motion correction.

---
 R/check_motion.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/check_motion.R b/R/check_motion.R
index 76f1d73..306c2df 100644
--- a/R/check_motion.R
+++ b/R/check_motion.R
@@ -58,7 +58,7 @@ check_motion <- function(rawdir = NULL, pattern = NULL, parfile = NULL,
 
 
   spikes <- apply(motion_data, 2, cdiff)
-  spikes[4:6] <- 100 * pi * spikes[4:6] / 360
+  spikes[, 1:3] <- 100 * pi * spikes[, 1:3] / 360
   has_spike <- rowSums(abs(spikes)) > 0.5
 
   motion_data <- motion_data |>
-- 
GitLab


From eabf6ad766e54fa0f07cfcf4dc37f618399618b3 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 10 Nov 2022 17:36:19 +0100
Subject: [PATCH 26/46] Fix spike detection and change defaults.

---
 R/check_motion.R | 2 +-
 R/rs_pipeline.R  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/check_motion.R b/R/check_motion.R
index 306c2df..a881816 100644
--- a/R/check_motion.R
+++ b/R/check_motion.R
@@ -59,7 +59,7 @@ check_motion <- function(rawdir = NULL, pattern = NULL, parfile = NULL,
 
   spikes <- apply(motion_data, 2, cdiff)
   spikes[, 1:3] <- 100 * pi * spikes[, 1:3] / 360
-  has_spike <- rowSums(abs(spikes)) > 0.5
+  has_spike <- rowSums(abs(spikes)) > spike_cutoff
 
   motion_data <- motion_data |>
     dplyr::mutate(
diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index d4ea45d..37217d0 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -110,7 +110,7 @@ rs_pipeline <- function(
     motion_file <- gsub(".nii.gz", ".par", motion_cor)
 
     motion_check <- check_motion(parfile = motion_file, cutoff = motion_cutoff,
-                                 plot = FALSE)
+                                 spike_cutoff = 1.5, plot = FALSE)
     to_remove <- c(1:3, motion_check$flag_motion, motion_check$flag_spike)
 
     if (motion_check$exceeds_motion > 3 ||
-- 
GitLab


From c6639ffcd802407518dde5ec45b64745450fb076 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 16 Nov 2022 14:42:08 +0100
Subject: [PATCH 27/46] Add dots to basic summary.

---
 R/basic_summary.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/basic_summary.R b/R/basic_summary.R
index 76b3c40..b34840c 100644
--- a/R/basic_summary.R
+++ b/R/basic_summary.R
@@ -8,6 +8,7 @@
 #' @param whole_graph If measure characterises for the entire graph,
 #'   this should be set to true.
 #' @param outname Name for the grouping variable in the output.
+#' @param ... Further variables to group by.
 #'
 #' If no measure is given the data is grouped by groups in the subjects
 #' table.
@@ -18,13 +19,13 @@
 #' @export
 basic_summary <- function(datalist, subjects, id_var, group_var,
                           measure = NULL, whole_graph = FALSE,
-                          outname = "group") {
+                          outname = "group", ...) {
   split_tbls <- split_graph_list(datalist, subjects)
   gsym <- rlang::sym(outname)
 
   groups <- subjects %>%
     dplyr::rename({{ outname }} := {{ group_var }}) %>%
-    dplyr::group_by({{ gsym }}) %>%
+    dplyr::group_by({{ gsym }}, ...) %>%
     dplyr::group_keys()
 
   if (whole_graph) {
-- 
GitLab


From 085857f79acaa39e6363f596b3ff535ad7a2c4d5 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <christian.hohenfeld@rwth-aachen.de>
Date: Wed, 16 Nov 2022 16:05:14 +0100
Subject: [PATCH 28/46] Revert "Add dots to basic summary."

This reverts commit c6639ffcd802407518dde5ec45b64745450fb076
---
 R/basic_summary.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/basic_summary.R b/R/basic_summary.R
index b34840c..76b3c40 100644
--- a/R/basic_summary.R
+++ b/R/basic_summary.R
@@ -8,7 +8,6 @@
 #' @param whole_graph If measure characterises for the entire graph,
 #'   this should be set to true.
 #' @param outname Name for the grouping variable in the output.
-#' @param ... Further variables to group by.
 #'
 #' If no measure is given the data is grouped by groups in the subjects
 #' table.
@@ -19,13 +18,13 @@
 #' @export
 basic_summary <- function(datalist, subjects, id_var, group_var,
                           measure = NULL, whole_graph = FALSE,
-                          outname = "group", ...) {
+                          outname = "group") {
   split_tbls <- split_graph_list(datalist, subjects)
   gsym <- rlang::sym(outname)
 
   groups <- subjects %>%
     dplyr::rename({{ outname }} := {{ group_var }}) %>%
-    dplyr::group_by({{ gsym }}, ...) %>%
+    dplyr::group_by({{ gsym }}) %>%
     dplyr::group_keys()
 
   if (whole_graph) {
-- 
GitLab


From 4f43f4cfb06d5ce5459e83d41fdec2df5941cfb0 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Fri, 18 Nov 2022 09:07:47 +0100
Subject: [PATCH 29/46] Handle spike removal in a better way.

---
 R/rs_pipeline.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index 37217d0..b09013f 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -111,7 +111,6 @@ rs_pipeline <- function(
 
     motion_check <- check_motion(parfile = motion_file, cutoff = motion_cutoff,
                                  spike_cutoff = 1.5, plot = FALSE)
-    to_remove <- c(1:3, motion_check$flag_motion, motion_check$flag_spike)
 
     if (motion_check$exceeds_motion > 3 ||
         motion_check$exceeds_spike > min(
@@ -239,7 +238,8 @@ rs_pipeline <- function(
     rs_filtered <- tibble::as_tibble(rs_filtered)
 
     print_msg("Scrub time series...")
-    rs_filtered <- rs_filtered[-to_remove, ]
+    rs_filtered[c(motion_check$flag_motion, motion_check$flag_spike)] <- NA_real_
+    rs_filtered <- rs_filtered[-c(1:3), ]
 
     rs_list <- list()
     rs_list$time_course <- rs_filtered
@@ -249,7 +249,7 @@ rs_pipeline <- function(
     corsym <- rlang::sym("cor")
 
     print_msg("Correlating...")
-    rs_cor <- stats::cor(rs_filtered)
+    rs_cor <- stats::cor(rs_filtered, use = "complete.obs")
     rs_cor <- tibble::as_tibble(rs_cor, rownames = "x1") %>%
         tidyr::gather(!!x2sym, !!corsym, -!!x1sym)
 
-- 
GitLab


From 1b8353f452a9265d450a69433f7f13a565cef8b7 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 30 Nov 2022 15:17:10 +0100
Subject: [PATCH 30/46] reformat.

---
 R/compare_measure_group.R | 53 +++++++++++++++++++--------------------
 1 file changed, 26 insertions(+), 27 deletions(-)

diff --git a/R/compare_measure_group.R b/R/compare_measure_group.R
index d3e1f66..4142925 100644
--- a/R/compare_measure_group.R
+++ b/R/compare_measure_group.R
@@ -9,41 +9,40 @@
 #' @export
 compare_measure_group <- function(rawlist, dv, ..., add_name = FALSE,
                                   remove = NULL) {
-  grplist <- lapply(seq_along(rawlist),
-                    function(x) {
-                      rawlist[[x]]$group <- names(rawlist)[x]
-                      rawlist[[x]]
-                    })
-  grplist <- do.call("rbind", grplist)
+    grplist <- lapply(seq_along(rawlist), function(x) {
+                    rawlist[[x]]$group <- names(rawlist)[x]
+                    rawlist[[x]]
+                })
+    grplist <- do.call("rbind", grplist)
 
-  if (!is.null(remove)) {
-    grplist <- grplist %>% dplyr::filter(.data$group != remove)
-  }
+    if (!is.null(remove)) {
+        grplist <- grplist %>% dplyr::filter(.data$group != remove)
+    }
 
-  additional_formula <- paste(..., sep = "+")
-  additional_formula <- ifelse(length(additional_formula) == 0, "",
-                               paste0("+", additional_formula))
+    additional_formula <- paste(..., sep = "+")
+    additional_formula <- ifelse(length(additional_formula) == 0, "",
+                                 paste0("+", additional_formula))
 
-  if (add_name) {
-    frml <- stats::as.formula(paste(dv, "~ group * name", additional_formula))
-  } else {
-    frml <- stats::as.formula(paste(dv, " ~ group", additional_formula))
-  }
-  mod <- stats::lm(frml, data = grplist)
-  modtbl <- mod %>%
-    broom::tidy() %>%
-    dplyr::mutate(s.value = -log2(.data$p.value))
+    if (add_name) {
+        frml <- stats::as.formula(paste(dv, "~ group * name", additional_formula))
+    } else {
+        frml <- stats::as.formula(paste(dv, " ~ group", additional_formula))
+    }
+    mod <- stats::lm(frml, data = grplist)
+    modtbl <- mod %>%
+        broom::tidy() %>%
+        dplyr::mutate(s.value = -log2(.data$p.value))
 
   av <- car::Anova(mod, type = 3)
   tbl <- av %>%
     broom::tidy() %>%
     dplyr::mutate(s.value = -log2(.data$p.value))
 
-  bayes <- rstanarm::stan_glm(frml, data = grplist, iter = 2000, refresh = 0)
-  bayes_tbl <- parameters::model_parameters(bayes,
-                                            test = c("pd", "rope", "bf"))
+    bayes <- rstanarm::stan_glm(frml, data = grplist, iter = 2000, refresh = 0)
+    bayes_tbl <- parameters::model_parameters(
+        bayes, test = c("pd", "rope", "bf"))
 
-  list(lm = mod, lm_tbl = modtbl,
-       anova = av, anova_tbl = tbl,
-       bayesian = bayes, bayesian_tbl = bayes_tbl)
+    list(lm = mod, lm_tbl = modtbl,
+         anova = av, anova_tbl = tbl,
+         bayesian = bayes, bayesian_tbl = bayes_tbl)
 }
-- 
GitLab


From 75cf08b03bc7ab3ab7de92441d129d58693d4aca Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 30 Nov 2022 15:17:19 +0100
Subject: [PATCH 31/46] make anova optional.

---
 R/compare_measure_group.R | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/R/compare_measure_group.R b/R/compare_measure_group.R
index 4142925..3dfb8b9 100644
--- a/R/compare_measure_group.R
+++ b/R/compare_measure_group.R
@@ -33,10 +33,15 @@ compare_measure_group <- function(rawlist, dv, ..., add_name = FALSE,
         broom::tidy() %>%
         dplyr::mutate(s.value = -log2(.data$p.value))
 
-  av <- car::Anova(mod, type = 3)
-  tbl <- av %>%
-    broom::tidy() %>%
-    dplyr::mutate(s.value = -log2(.data$p.value))
+    if (anova) {
+        av <- car::Anova(mod, type = 3)
+        tbl <- av %>%
+            broom::tidy() %>%
+            dplyr::mutate(s.value = -log2(.data$p.value))
+    } else {
+        av <- NA
+        tbl <- NA
+    }
 
     bayes <- rstanarm::stan_glm(frml, data = grplist, iter = 2000, refresh = 0)
     bayes_tbl <- parameters::model_parameters(
-- 
GitLab


From 6ffcfc4ac00462111ff571897b4c8fc8c9b1cc0a Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 30 Nov 2022 15:52:42 +0100
Subject: [PATCH 32/46] Update remotes.

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f6d0a92..16f2e3e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -41,6 +41,6 @@ Suggests:
     withr
 Remotes:
     gitlab::choh/littlehelpers,
-    gitlab::choh/rsfmri
+    git::https://git.rwth-aachen.de/christian.hohenfeld/rsfmri.git
 Depends: 
     R (>= 2.10)
-- 
GitLab


From e72c32d1395f0ace129bad4669ae7bd6579fd266 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Wed, 30 Nov 2022 15:54:27 +0100
Subject: [PATCH 33/46] Make ANOVA actually optional.

---
 R/compare_measure_group.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/compare_measure_group.R b/R/compare_measure_group.R
index 3dfb8b9..0a5363e 100644
--- a/R/compare_measure_group.R
+++ b/R/compare_measure_group.R
@@ -8,7 +8,7 @@
 #' @importFrom rlang .data
 #' @export
 compare_measure_group <- function(rawlist, dv, ..., add_name = FALSE,
-                                  remove = NULL) {
+                                  remove = NULL, anova = TRUE) {
     grplist <- lapply(seq_along(rawlist), function(x) {
                     rawlist[[x]]$group <- names(rawlist)[x]
                     rawlist[[x]]
-- 
GitLab


From cba6a3dccca708f1e9ce92124a7d99bf7193fc7c Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 1 Dec 2022 12:19:44 +0100
Subject: [PATCH 34/46] Fix CI

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index beb6c1e..7bee86f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,7 +6,7 @@ stages:
 
 before_script:
   - apt-get update
-  - apt-get --yes install libglpk-dev
+  - apt-get --yes install libglpk-dev libicu-dev
   - mkdir -p rlib
   - echo 'R_LIBS="rlib"' > .Renviron
   - echo 'R_LIBS_USER="rlib"' >> .Renviron
@@ -14,7 +14,7 @@ before_script:
 
 cache:
     key: r-library
-    paths: 
+    paths:
       - rlib
 
 prep:
-- 
GitLab


From d879a82eb4d6353e5ae45c8d442cfde4347d1170 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 1 Dec 2022 12:33:56 +0100
Subject: [PATCH 35/46] Try installing stringr manually.

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7bee86f..ebb6b9d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,7 +21,7 @@ prep:
   stage: .pre
   script:
     - R --version
-    - R -e "install.packages(c('devtools', 'usethis'))"
+    - R -e "install.packages(c('devtools', 'usethis', 'stringr'))"
     - R -e "devtools::install_gitlab('choh/littlehelpers')"
     - R -e "devtools::install_gitlab('choh/rsfmri')"
     - R -e "devtools::install_deps(dependencies = TRUE)"
-- 
GitLab


From 63c3299efbd290284687c4ba8a44986bf86e45a4 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 1 Dec 2022 12:41:52 +0100
Subject: [PATCH 36/46] Try forcing source installation.

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ebb6b9d..9c3dea4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,7 +21,7 @@ prep:
   stage: .pre
   script:
     - R --version
-    - R -e "install.packages(c('devtools', 'usethis', 'stringr'))"
+    - R -e "install.packages(c('devtools', 'usethis'), type = 'source')"
     - R -e "devtools::install_gitlab('choh/littlehelpers')"
     - R -e "devtools::install_gitlab('choh/rsfmri')"
     - R -e "devtools::install_deps(dependencies = TRUE)"
-- 
GitLab


From 740cdfa664822fc9e8c677e365e76948071e70df Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 1 Dec 2022 12:55:49 +0100
Subject: [PATCH 37/46] try forcing source repo.

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9c3dea4..716976c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,7 +21,7 @@ prep:
   stage: .pre
   script:
     - R --version
-    - R -e "install.packages(c('devtools', 'usethis'), type = 'source')"
+    - R -e "install.packages(c('devtools', 'usethis'), type = 'source', repos = 'https://cran.uni-muenster.de/')"
     - R -e "devtools::install_gitlab('choh/littlehelpers')"
     - R -e "devtools::install_gitlab('choh/rsfmri')"
     - R -e "devtools::install_deps(dependencies = TRUE)"
-- 
GitLab


From bc88d1691f9736ce116c7e3c89fb34b6b5e46d83 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <christian.hohenfeld@rwth-aachen.de>
Date: Thu, 1 Dec 2022 13:03:52 +0100
Subject: [PATCH 38/46] Update .gitlab-ci.yml

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 716976c..66f9014 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,7 +21,7 @@ prep:
   stage: .pre
   script:
     - R --version
-    - R -e "install.packages(c('devtools', 'usethis'), type = 'source', repos = 'https://cran.uni-muenster.de/')"
+    - R -e "install.packages(c('devtools', 'usethis', 'stringr'), type = 'source', repos = 'https://cran.uni-muenster.de/')"
     - R -e "devtools::install_gitlab('choh/littlehelpers')"
     - R -e "devtools::install_gitlab('choh/rsfmri')"
     - R -e "devtools::install_deps(dependencies = TRUE)"
-- 
GitLab


From e148bbdfd1931c576ca63d47a0c5197d65f5f9f4 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <christian.hohenfeld@rwth-aachen.de>
Date: Thu, 1 Dec 2022 13:10:39 +0100
Subject: [PATCH 39/46] Update .gitlab-ci.yml

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 66f9014..6ef0241 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,7 +21,7 @@ prep:
   stage: .pre
   script:
     - R --version
-    - R -e "install.packages(c('devtools', 'usethis', 'stringr'), type = 'source', repos = 'https://cran.uni-muenster.de/')"
+    - R -e "install.packages(c('stringi', 'devtools', 'usethis', 'stringr'), type = 'source', repos = 'https://cran.uni-muenster.de/')"
     - R -e "devtools::install_gitlab('choh/littlehelpers')"
     - R -e "devtools::install_gitlab('choh/rsfmri')"
     - R -e "devtools::install_deps(dependencies = TRUE)"
-- 
GitLab


From b5e5e541ca746b9d163e8a3c788bc20c9740db60 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <christian.hohenfeld@rwth-aachen.de>
Date: Thu, 1 Dec 2022 13:14:53 +0100
Subject: [PATCH 40/46] Update .gitlab-ci.yml

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6ef0241..22aa3cb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -23,7 +23,7 @@ prep:
     - R --version
     - R -e "install.packages(c('stringi', 'devtools', 'usethis', 'stringr'), type = 'source', repos = 'https://cran.uni-muenster.de/')"
     - R -e "devtools::install_gitlab('choh/littlehelpers')"
-    - R -e "devtools::install_gitlab('choh/rsfmri')"
+    - R -e "devtools::install_git('https://git.rwth-aachen.de/christian.hohenfeld/rsfmri.git')"
     - R -e "devtools::install_deps(dependencies = TRUE)"
     - R -e "devtools::install()"
 
-- 
GitLab


From 860bbc3182fb27c46d020ea7924bff7c3a2aa8a8 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <christian.hohenfeld@rwth-aachen.de>
Date: Thu, 1 Dec 2022 13:20:53 +0100
Subject: [PATCH 41/46] Update .gitlab-ci.yml

---
 .gitlab-ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 22aa3cb..f633ba7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -24,7 +24,6 @@ prep:
     - R -e "install.packages(c('stringi', 'devtools', 'usethis', 'stringr'), type = 'source', repos = 'https://cran.uni-muenster.de/')"
     - R -e "devtools::install_gitlab('choh/littlehelpers')"
     - R -e "devtools::install_git('https://git.rwth-aachen.de/christian.hohenfeld/rsfmri.git')"
-    - R -e "devtools::install_deps(dependencies = TRUE)"
     - R -e "devtools::install()"
 
 lintr:
-- 
GitLab


From 3030447bcf167fdd70adb7b3884d3b2386772b33 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <christian.hohenfeld@rwth-aachen.de>
Date: Thu, 1 Dec 2022 13:35:29 +0100
Subject: [PATCH 42/46] Update .gitlab-ci.yml

---
 .gitlab-ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f633ba7..078d973 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,9 +21,9 @@ prep:
   stage: .pre
   script:
     - R --version
-    - R -e "install.packages(c('stringi', 'devtools', 'usethis', 'stringr'), type = 'source', repos = 'https://cran.uni-muenster.de/')"
-    - R -e "devtools::install_gitlab('choh/littlehelpers')"
-    - R -e "devtools::install_git('https://git.rwth-aachen.de/christian.hohenfeld/rsfmri.git')"
+    - R -e "install.packages(c('remotes', 'stringi', 'devtools', 'usethis', 'stringr'), type = 'source', repos = 'https://cran.uni-muenster.de/')"
+    - R -e "remotes::install_gitlab('choh/littlehelpers')"
+    - R -e "remotes::install_git('https://git.rwth-aachen.de/christian.hohenfeld/rsfmri.git')"
     - R -e "devtools::install()"
 
 lintr:
-- 
GitLab


From 3d22bccbbc2f73724d047328dabf34c74d9f896c Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <christian.hohenfeld@rwth-aachen.de>
Date: Thu, 1 Dec 2022 13:57:24 +0100
Subject: [PATCH 43/46] Update .gitlab-ci.yml file

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 078d973..8c03b2c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,7 +21,7 @@ prep:
   stage: .pre
   script:
     - R --version
-    - R -e "install.packages(c('remotes', 'stringi', 'devtools', 'usethis', 'stringr'), type = 'source', repos = 'https://cran.uni-muenster.de/')"
+    - R -e "install.packages(c('remotes', 'stringi', 'devtools', 'usethis', 'stringr', 'lintr'), type = 'source', repos = 'https://cran.uni-muenster.de/')"
     - R -e "remotes::install_gitlab('choh/littlehelpers')"
     - R -e "remotes::install_git('https://git.rwth-aachen.de/christian.hohenfeld/rsfmri.git')"
     - R -e "devtools::install()"
-- 
GitLab


From 92e9d9acfb767bd9e6d7df0671246b97bfc75585 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 1 Dec 2022 14:32:19 +0100
Subject: [PATCH 44/46] Handle linter errors

---
 R/compare_measure_group.R |  3 ++-
 R/rs_pipeline.R           | 13 ++++++++-----
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/R/compare_measure_group.R b/R/compare_measure_group.R
index 0a5363e..808ce1b 100644
--- a/R/compare_measure_group.R
+++ b/R/compare_measure_group.R
@@ -24,7 +24,8 @@ compare_measure_group <- function(rawlist, dv, ..., add_name = FALSE,
                                  paste0("+", additional_formula))
 
     if (add_name) {
-        frml <- stats::as.formula(paste(dv, "~ group * name", additional_formula))
+        frml <- stats::as.formula(
+            paste(dv, "~ group * name", additional_formula))
     } else {
         frml <- stats::as.formula(paste(dv, " ~ group", additional_formula))
     }
diff --git a/R/rs_pipeline.R b/R/rs_pipeline.R
index b09013f..1eacfc2 100644
--- a/R/rs_pipeline.R
+++ b/R/rs_pipeline.R
@@ -25,6 +25,7 @@
 #'
 #' @return A list containing time courses and a pairwise correlation matrix.
 #' @export
+# nolint start: cyclocomp_linter
 rs_pipeline <- function(
         functional,
         anatomy,
@@ -71,14 +72,14 @@ rs_pipeline <- function(
 
     mag_path <- NULL
     pha_path <- NULL
-    if (!is.null(magnitude_map) | !is.null(phase_map)) {
+    if (!is.null(magnitude_map) || !is.null(phase_map)) {
         mag_path <- copy_to_temp(magnitude_map, temp_dir)
         pha_path <- copy_to_temp(phase_map, temp_dir)
     }
 
     ap_path <- NULL
     pa_path <- NULL
-    if (!is.null(ap_map) | !is.null(pa_map)) {
+    if (!is.null(ap_map) || !is.null(pa_map)) {
         ap_path <- copy_to_temp(ap_map, temp_dir)
         pa_path <- copy_to_temp(pa_map, temp_dir)
     }
@@ -125,11 +126,11 @@ rs_pipeline <- function(
     map_mag_pha <- all(c(!is.null(magnitude_map), !is.null(phase_map)))
     map_ap_pa <- all(c(!is.null(ap_path), !is.null(pa_path)))
 
-    if (map_mag_pha & map_ap_pa) {
+    if (map_mag_pha && map_ap_pa) {
         stop("Either use Mag/Pha map or AP/PA, not both.")
     }
 
-    if (map_mag_pha | map_ap_pa) {
+    if (map_mag_pha || map_ap_pa) {
         print_msg("Generating Field Map...")
         if (map_mag_pha) {
             fm <- rsfmri::fsl_make_fieldmap(mag_path, pha_path, echo_spacing)
@@ -238,7 +239,8 @@ rs_pipeline <- function(
     rs_filtered <- tibble::as_tibble(rs_filtered)
 
     print_msg("Scrub time series...")
-    rs_filtered[c(motion_check$flag_motion, motion_check$flag_spike)] <- NA_real_
+    rs_filtered[c(
+        motion_check$flag_motion, motion_check$flag_spike)] <- NA_real_
     rs_filtered <- rs_filtered[-c(1:3), ]
 
     rs_list <- list()
@@ -266,3 +268,4 @@ rs_pipeline <- function(
     print_msg("Done.")
     rs_list
 }
+# nolint end
-- 
GitLab


From 6f369f33fb8e5d0f89ca3326cec6ceeaecec3ff5 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 1 Dec 2022 14:32:26 +0100
Subject: [PATCH 45/46] Update docs.

---
 R/compare_measure_group.R    |  1 +
 man/compare_measure_group.Rd | 11 ++++++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/R/compare_measure_group.R b/R/compare_measure_group.R
index 808ce1b..2a23b3b 100644
--- a/R/compare_measure_group.R
+++ b/R/compare_measure_group.R
@@ -5,6 +5,7 @@
 #' @param ... Strings giving variables to include in the model formula.
 #' @param add_name Whether to add interaction term group x name, default FALSE
 #' @param remove Name of a group to remove
+#' @param anova Logical value specifying whether to compute an ANOVA.
 #' @importFrom rlang .data
 #' @export
 compare_measure_group <- function(rawlist, dv, ..., add_name = FALSE,
diff --git a/man/compare_measure_group.Rd b/man/compare_measure_group.Rd
index 4e2ca80..51aa314 100644
--- a/man/compare_measure_group.Rd
+++ b/man/compare_measure_group.Rd
@@ -4,7 +4,14 @@
 \alias{compare_measure_group}
 \title{Compare a measure between groups.}
 \usage{
-compare_measure_group(rawlist, dv, ..., add_name = FALSE, remove = NULL)
+compare_measure_group(
+  rawlist,
+  dv,
+  ...,
+  add_name = FALSE,
+  remove = NULL,
+  anova = TRUE
+)
 }
 \arguments{
 \item{rawlist}{A list of graphs split by groups.}
@@ -16,6 +23,8 @@ compare_measure_group(rawlist, dv, ..., add_name = FALSE, remove = NULL)
 \item{add_name}{Whether to add interaction term group x name, default FALSE}
 
 \item{remove}{Name of a group to remove}
+
+\item{anova}{Logical value specifying whether to compute an ANOVA.}
 }
 \description{
 Compare a measure between groups.
-- 
GitLab


From 9f26a7afe7f635192ff42ff22fa73ad2572e1ce7 Mon Sep 17 00:00:00 2001
From: Christian Hohenfeld <git@hohenfeld.is>
Date: Thu, 1 Dec 2022 15:12:47 +0100
Subject: [PATCH 46/46] Bump version number.

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 16f2e3e..ee79766 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rsAnalysis
 Title: High-Level Tools for rsfMRI analysis
-Version: 0.4.5.9000
+Version: 0.4.6
 Authors@R: 
     person(given = "Christian",
            family = "Hohenfeld",
-- 
GitLab