new nki stuff; setup subject lists; run subdists

nki/03_post-process/22_funcpaths_to_4mm.bash

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+cd /home2/data/Projects/CWAS/share/nki/subinfo
+
+strategies=("compcor" "global")
+scans=( "short" "medium" "long" )
+scan_folder=("40_Set1_N104" "40_Set1_N104" "40_Set2_N92")
+
+for strategy in ${strategies}; do
+    echo "strategy: ${strategy}"
+    for i in $( count -digits 1 0 2); do
+        scan=${scans[$i]}
+        folder=${scan_folder[$i]}
+        echo "  scan: ${scan}"
+
+        inpath="${folder}/${scan}_${strategy}_funcpaths.txt"
+        outpath="${folder}/${scan}_${strategy}_funcpaths_4mm.txt"
+        sed s/functional_mni/functional_mni_4mm/g ${inpath} > ${outpath}        
+    done
+done

nki/03_post-process/24_generate_mask_4mm.R

@@ -0,0 +1,72 @@
+#!/usr/bin/env Rscript
+
+# This script generates brain mask for each subject in 4mm space
+# and then creates the group brain mask
+
+library(connectir)
+
+###
+# Setup
+###
+
+# Paths
+basedir <- "/home2/data/Projects/CWAS/share/nki"
+subinfo <- file.path(basedir, "subinfo")
+roidir <- "/home2/data/Projects/CWAS/nki/rois"
+
+# Scan stuff
+scans <- c("short", "medium", "long")
+scan_folder <- c("40_Set1_N104", "40_Set1_N104", "40_Set2_N92")
+
+# Other
+strategies <- c("compcor", "global")
+strategy <- strategies[1]
+
+
+###
+# Do it
+###
+
+maskfiles <- lapply(1:length(scans), function(si) {
+    vcat(T, "scan: %s", scans[si])
+
+    ## Individual Subjects
+    vcat(T, "...individual subjects")
+    flist <- file.path(subinfo, scan_folder[si], sprintf("%s_%s_funcpaths_4mm.txt", scans[si], strategy))
+    raw <- read.table(flist)[,1]
+    funcpaths <- as.character(raw)
+    funcpaths <- sub("/home/", "/home2/", funcpaths)
+
+    cmd <- "fslmaths %s -Tstd -abs -bin %s"
+    maskfiles <- sapply(funcpaths, function(funcpath) {
+        outdir <- dirname(dirname(funcpath))
+        outfile <- file.path(outdir, "functional_brain_mask_to_standard_4mm.nii.gz")
+        real_cmd <- sprintf(cmd, funcpath, outfile)
+
+        if (file.exists(outfile)) {
+            cat("skipping, file exists", outfile, "\n")
+            return(outfile)
+        } else {
+            cat(real_cmd, "\n")
+            system(real_cmd)
+            return(outfile)
+        }
+    })
+
+    return(maskfiles)
+})
+maskfiles <- unlist(maskfiles)
+
+
+## Group Mask
+vcat(T, "...group mask")
+outfile <- file.path(roidir, "mask_gray_4mm.nii.gz")
+std_mask_file <- file.path(roidir, "grey_matter_4mm.nii.gz")
+
+hdr <- read.nifti.header(std_mask_file)
+overlap_mask <- read.mask(std_mask_file)
+
+for (maskfile in maskfiles)
+    overlap_mask <- overlap_mask & read.mask(maskfile)
+
+write.nifti(overlap_mask*1, hdr, outfile=outfile, odt="int")

nki/03_post-process/16_create_random_clusters_2mm.py → nki/03_post-process/26_create_random_clusters_4mm.py

@@ -26,7 +26,7 @@
 
 # name of the maskfile that we will be using
 roidir = "/home2/data/Projects/CWAS/nki/rois"
-maskfile = path.join(roidir, "mask_gray_2mm.nii.gz")
+maskfile = path.join(roidir, "mask_gray_4mm.nii.gz")
 
 
 ###
@@ -46,7 +46,7 @@
 print "3. Clustering"
 
 from binfile_parcellation import *
-  
+
 ks = [25,50,100,200,400,800,1600,3200,6400]
 
 # For random custering, this is all we need to do, there is no need for group

nki/03_post-process/28_extract_rois_4mm.R

@@ -0,0 +1,100 @@
+#!/usr/bin/env Rscript
+
+# This script will extract the time-series from each of the ROI sets
+
+
+###
+# Setup
+###
+
+library(connectir)
+library(tools)
+
+# Paths
+basedir <- "/home2/data/Projects/CWAS/share/nki"
+subinfo <- file.path(basedir, "subinfo")
+
+# Scan stuff
+scans <- c("short", "medium", "long")
+scan_folder <- c("40_Set1_N104", "40_Set1_N104", "40_Set2_N92")
+
+# Other
+strategies <- c("compcor", "global")
+
+# ROI stuff
+rbase <- "/home2/data/Projects/CWAS/nki/rois"
+mask_file <- file.path(rbase, "mask_gray_4mm.nii.gz")
+ks <- c(25,50,100,200,400,800,1600,3200,6400)
+#ks <- c(3200)
+roi_files <- file.path(rbase, sprintf("rois_random_k%04i.nii.gz", ks))
+
+set_parallel_procs(nforks=1, nthreads=4)
+
+
+###
+# ROI Extraction (Random) with compcor
+###
+
+strategy <- "compcor"
+vcat(T, strategy)
+
+for (si in 1:length(scans)) {
+    # Paths to functionals
+    fn <- file.path(subinfo, scan_folder[si], 
+                    sprintf("%s_%s_funcpaths_4mm.txt", scans[si], strategy))
+    func_files <- read.table(fn)[,1]
+    func_files <- as.character(func_files)
+
+    # Go through ROIs
+    for (roi_file in roi_files) {
+        vcat(T, "ROI: %s", roi_file)
+        roi_base <- file_path_sans_ext(file_path_sans_ext(basename(roi_file)))
+        out_files <- sapply(func_files, function(func_file) {
+            out_file <- file.path(dirname(func_file), 
+                                  paste(roi_base, ".nii.gz", sep=""))
+            if (!file.exists(out_file)) {
+                roi_mean_wrapper(func_file, roi_file, mask_file, out_file)
+            }
+            return(out_file)
+        })
+        out_files <- unlist(out_files)
+
+        ofile <- file.path(subinfo, scan_folder[si], sprintf("%s_%s_%s.txt", scans[si], strategy, roi_base))
+        write.table(out_files, file=ofile, row.names=F, col.names=F)
+    }
+}
+
+
+
+####
+## ROI Extraction (Random) with global
+####
+#
+#strategy <- "global"
+#vcat(T, strategy)
+#
+#for (si in 1:length(scans)) {
+#    # Paths to functionals
+#    fn <- file.path(subinfo, scan_folder[si], 
+#                    sprintf("%s_%s_funcpaths.txt", scans[si], strategy))
+#    func_files <- read.table(fn)[,1]
+#    func_files <- as.character(func_files)
+#    
+#    # Go through ROIs
+#    for (roi_file in roi_files) {
+#        vcat(T, "ROI: %s", roi_file)
+#        roi_base <- file_path_sans_ext(file_path_sans_ext(basename(roi_file)))
+#        out_files <- sapply(func_files, function(func_file) {
+#            out_file <- file.path(dirname(func_file), paste(roi_base, ".nii.gz", sep=""))
+#            roi_mean_wrapper(func_file, roi_file, mask_file, out_file)
+#            return(out_file)
+#        })
+#        out_files <- unlist(out_files)
+#        
+#        ofile <- file.path(subinfo, scan_folder[si], sprintf("%s_%s_%s.txt", scans[si], strategy, roi_base))
+#        write.table(out_files, file=ofile, row.names=F, col.names=F)
+#    }
+#}
+
+
+

nki/03_post-process/30_drop_bad_participant.R

@@ -0,0 +1,57 @@
+#!/usr/bin/env Rscript
+
+# This script will take out the participant below from everything!
+# and then resave
+
+# Paths
+basedir <- "/home2/data/Projects/CWAS/share/nki"
+subinfo <- file.path(basedir, "subinfo")
+roidir <- "/home2/data/Projects/CWAS/nki/rois"
+
+# Scan stuff
+scan_folders <- c("40_Set1_N104", "40_Set2_N92")
+
+# Subject
+bad_subject <- "M10982376"
+
+# Loop through
+for (folder in scan_folders) {
+    cat("changing directory\n")
+    cat(file.path(subinfo, folder), "\n")
+    setwd(file.path(subinfo, folder))
+
+    txt_files <- list.files(pattern="txt$")
+    csv_files <- list.files(pattern="csv$")
+
+    if (!file.exists("archive")) {
+        cat("creating + copying stuff\n")
+        dir.create("archive", FALSE)
+        file.copy(txt_files, file.path("archive", txt_files))
+        file.copy(csv_files, file.path("archive", csv_files))
+    }
+
+    cat("textify\n")
+    for (txt_file in txt_files) {
+        cat("-", txt_file, "\n")
+        txt <- as.character(read.table(txt_file)[,1])
+        find <- grep(bad_subject, txt)
+        if (length(find) > 0) {
+            cat("-- replacing\n")
+            txt <- txt[-find]
+            write.table(txt, file=txt_file)
+        }
+    }
+
+    cat("csvify\n")
+    for (csv_file in csv_files) {
+        cat("-", csv_file, "\n")
+        csv <- read.csv(csv_file)
+        find <- grep(bad_subject, csv$Id)
+        if (length(find) > 0) {
+            cat("-- replacing\n")
+            csv <- csv[-find,]
+            row.names(csv) <- 1:nrow(csv)
+            write.csv(csv, file=csv_file)
+        }
+    }
+}

nki/05_cwas/ /input_funcs/scan0001.nii.gz

@@ -0,0 +1 @@
+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10902157_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0002.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10905290_RFA_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0003.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10905488_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0004.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10905521_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0005.nii.gz

@@ -0,0 +1 @@
+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10906057_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0006.nii.gz

@@ -0,0 +1 @@
+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10906780_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0007.nii.gz

@@ -0,0 +1 @@
+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10908355_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0008.nii.gz

@@ -0,0 +1 @@
+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10909727_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0009.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10911282_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0010.nii.gz

@@ -0,0 +1 @@
+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10912249_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0011.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10913013_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0012.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10914232_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0013.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10915321_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0014.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10915454_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0015.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10915564_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0016.nii.gz

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nki/05_cwas/ /input_funcs/scan0017.nii.gz

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nki/05_cwas/ /input_funcs/scan0018.nii.gz

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nki/05_cwas/ /input_funcs/scan0019.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10917168_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0020.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10918051_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0021.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10919866_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0022.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10922512_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0023.nii.gz

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nki/05_cwas/ /input_funcs/scan0024.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10923173_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0025.nii.gz

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nki/05_cwas/ /input_funcs/scan0026.nii.gz

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nki/05_cwas/ /input_funcs/scan0027.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10925762_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0028.nii.gz

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+/home/data/Projects/NKI_ROCKLAND_CPAC_test/Sink/sym_links/pipeline_OakhurstCity/_compcor_ncomponents_5_linear1.motion1.compcor1.CSF_0.98_GM_0.7_WM_0.98/M10931127_session_1/scan_RfMRI_mx_645_rest_RPI/func/bandpass_freqs_0.009.0.1/rois_random_k3200.nii.gz

nki/05_cwas/ /input_funcs/scan0029.nii.gz

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nki/05_cwas/ /input_funcs/scan0030.nii.gz

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