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| #!/usr/bin/env Rscript | ||
| args = commandArgs(trailingOnly=TRUE) | ||
| # Create masked GM matrix (subj x voxels) for OPNMF analyses # | ||
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| ### Arguments ### | ||
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| # 1: Species investigated - "chimp" or "human" | ||
| # 2: Name of meta data .csv file # | ||
| # 3: Name and relative path of GM mask Nifti image # | ||
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| wd <- "~/projects/chimp_human_opnmf/" | ||
| setwd(wd) | ||
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| # load in libraries needed for script # | ||
| # need to install pacman if not already installed | ||
| if (!require("pacman")) install.packages("pacman") | ||
| pacman::p_load(fs, readr, dplyr, neurobase, oro.nifti) | ||
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| # sample species either human (IXI) or chimp for locating images and naming outputs # | ||
| cohort <- args[1] # "chimp" or "human | ||
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| # sample meta data to gather image names # | ||
| meta_name <- args[2] #"Chimp_meta_QC_u50_n189.csv" | ||
| meta_data <- read_csv(file = paste(path_wd(), "data", cohort, meta_name, | ||
| sep = "/")) | ||
| # smoothing kernel of images - chimp 4mm & IXI 6mm # | ||
| if (cohort == "chimp") { | ||
| s_kernel <- "s4" | ||
| } else if (cohort == "human") { | ||
| s_kernel <- "s6" | ||
| } else { | ||
| print("!! ERROR don't recognise species given should be chimp or human !!") | ||
| } | ||
| # file names of images to create GM data matrix # | ||
| subj_name <- c(paste0(s_kernel, "_mwp1", meta_data$Subject, ".gz")) | ||
| # path to images# | ||
| img_path <- paste(path_wd(), "data", cohort, "mwp1", sep = "/") | ||
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| # create GM index at TPM 0.3GM # | ||
| mask_name <- args[3] #"masks/Chimp_GM_TPM_03_Cortex_2mm.nii.gz" | ||
| GM_mask <- readnii(paste(path_wd(), mask_name ,sep = "/")) | ||
| # GM index mask vector # | ||
| GM_ind <- c(img_data(GM_mask > 0)) | ||
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| # empty lists # | ||
| imgs <- vector(mode = "list", length = nrow(meta_data)) | ||
| imgs_GM <- vector(mode = "list", length = nrow(meta_data)) | ||
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| # fill lists with GM data from each subject # | ||
| for (i in 1:length(subj_name)) { | ||
| # read nifti images # | ||
| imgs[[i]] <- readnii(paste(img_path, subj_name[i], sep= "/")) | ||
| # mask GM data # | ||
| imgs_GM[[i]] <- c(img_data(imgs[[i]])[GM_ind]) | ||
| } | ||
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| # create a GM matrix subj x voxels # | ||
| GM_mat <- rbind(matrix(unlist(imgs_GM), | ||
| ncol = length(imgs_GM[[1]]), byrow = TRUE)) | ||
| # Name of outpu data matrix # | ||
| if (cohort == "chimp") { | ||
| out_name <- paste0("Chimp_cort_n", nrow(meta_data), "_TPM03_mat.rds") | ||
| } else if (cohort == "human") { | ||
| out_name <- paste0("IXI_cort_n", nrow(meta_data), "_mat.rds") | ||
| } else { | ||
| print("!! ERROR don't recognise species given should be chimp or human !!") | ||
| } | ||
| # save data matrix # | ||
| saveRDS(GM_mat, file = paste(path_wd(), "data", cohort, out_name, sep="/")) | ||
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| # Structural Preprocessing | ||
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| Structural preprocessing (T1-weighted images) for chimpanzee and human cohorts utilizing [SPM12](https://www.fil.ion.ucl.ac.uk/spm/software/spm12/) and [CAT12](http://www.neuro.uni-jena.de/cat/). The Matlab scripts are to be used as batch inputs to then adapted in the SPM batch editor. | ||
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| Following preprocessing move the ```mwp1*``` and smoothed modulated images into ```$project_dir/data/$cohort/wmp1/``` directory and then run the ```run_GM_matrix_create.sh``` to create the data matrix for OPNMF parcellation. | ||
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| clc, clear | ||
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| % ------------------------------------------------------------------------ | ||
| % Chimpanzee batch options that can be changed in the GUI or here directly | ||
| % ------------------------------------------------------------------------ | ||
| % open the chimpanzee preprocessing from cat12 | ||
| cat12('chimpanzee'); | ||
| % set the number of cores for parallel processing | ||
| try | ||
| numcores = max(cat_get_defaults('extopts.nproc'),1); | ||
| catch | ||
| numcores = 0; | ||
| end | ||
| %% CAT preprocessing | ||
| % ------------------------------------------------------------------------ | ||
| % Dir containing chimp original T1w images % | ||
| chimps_dir = ... | ||
| 'C:\Users\svickery\Documents\preproc_test'; | ||
| % chimp images % | ||
| chimp_img = dir(fullfile(chimps_dir,'*.nii')); | ||
| % IMG need to be in a cell to be read by batch % | ||
| for subj = 1:numel(chimp_img) | ||
| matlabbatch{1}.spm.tools.cat.estwrite.data{subj,1} = ... | ||
| fullfile(chimps_dir, chimp_img(subj).name); | ||
| end | ||
| % Check name and location of template dir in SPM dir % | ||
| % This should be the dir with cat v1725 | ||
| cattempdir = fullfile(spm('dir'),'toolbox','cat12','animal_templates'); | ||
| % CAT preprocessing expert options | ||
| % SPM parameter | ||
| matlabbatch{1}.spm.tools.cat.estwrite.data_wmh = {''}; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.nproc = numcores; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.opts.tpm = {fullfile(cattempdir,'chimpanzee_TPM.nii')}; % Juna chimp TPM | ||
| matlabbatch{1}.spm.tools.cat.estwrite.opts.affreg = 'none'; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.opts.ngaus = [1 1 2 3 4 2]; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.opts.warpreg = [0 0.001 0.5 0.05 0.2]; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.opts.bias.spm.biasfwhm = 30; % small values are important to remove the bias but 30 mm is more or less the limit | ||
| matlabbatch{1}.spm.tools.cat.estwrite.opts.bias.spm.biasreg = 0.001; % | ||
| matlabbatch{1}.spm.tools.cat.estwrite.opts.acc.spm.samp = 1.5; % ############# higher resolutions helps but takes much more time (e.g., 1.5 about 4 hours), so 1.0 to 1.5 mm seems to be adequate | ||
| matlabbatch{1}.spm.tools.cat.estwrite.opts.acc.spm.tol = 1e-06; % smaller values are better and important to remove the bias in some image | ||
| matlabbatch{1}.spm.tools.cat.estwrite.opts.redspmres = 0; | ||
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| % segmentation options | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.segmentation.APP = 1070; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.segmentation.NCstr = -Inf; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.segmentation.spm_kamap = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.segmentation.LASstr = 1.0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.segmentation.gcutstr = 2; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.segmentation.cleanupstr = 0.5; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.segmentation.BVCstr = 0.5; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.segmentation.WMHC = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.segmentation.SLC = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.segmentation.mrf = 1; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.segmentation.restypes.best = [0.5 0.3]; | ||
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| % registration options | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.T1 = {fullfile(cattempdir,'chimpanzee_T1.nii')}; % Juna chimp T1 | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.brainmask = {fullfile(cattempdir,'chimpanzee_brainmask.nii')}; % Juna chimp brainmask | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.cat12atlas = {fullfile(cattempdir,'chimpanzee_cat.nii')}; % Juna chimp cat atlas | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.darteltpm = {fullfile(cattempdir,'chimpanzee_Template_1.nii')}; % there is no Juna chimp Dartel template as shooting is much better | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.shootingtpm = {fullfile(cattempdir,'chimpanzee_Template_0_GS.nii')}; % Juna chimp shooting template | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.regstr = 0.5; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.vox = 2; % Downsample to 2mm for faster OPNMF processing | ||
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| % surface options | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.surface.pbtres = 0.5; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.surface.pbtmethod = 'pbt2x'; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.surface.pbtlas = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.surface.collcorr = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.surface.reduce_mesh = 1; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.surface.vdist = 1.33333333333333; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.surface.scale_cortex = 0.7; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.surface.add_parahipp = 0.1; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.surface.close_parahipp = 0; | ||
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| % admin options | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.admin.experimental = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.admin.new_release = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.admin.lazy = 0; % ############## avoid reprocessing | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.admin.ignoreErrors = 1; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.admin.verb = 2; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.extopts.admin.print = 2; | ||
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| % output options | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 0; % surface reconstruction - not yet optimised for non-human primates | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.surf_measures = 3; | ||
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| % volume atlas maps | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.chimpanzee_atlas_davi = 1; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.ownatlas = {''}; % you can add own atlas maps but they have to be in the same orientation as the other template files especially the final GS template | ||
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| % surface atlas maps | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.sROImenu.satlases.Desikan = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.sROImenu.satlases.Destrieux = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.sROImenu.satlases.HCP = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.sROImenu.satlases.Schaefer2018_100P_17N = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.sROImenu.satlases.Schaefer2018_200P_17N = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.sROImenu.satlases.Schaefer2018_400P_17N = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.sROImenu.satlases.Schaefer2018_600P_17N = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.sROImenu.satlases.ownatlas = {''}; | ||
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| % volume output | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.GM.native = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.GM.warped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.GM.mod = 1; % needed for VBM | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.GM.dartel = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.WM.native = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.WM.warped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.WM.mod = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.WM.dartel = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.native = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.warped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.mod = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.dartel = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.bias.native = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.bias.warped = 1; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.bias.dartel = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.jacobianwarped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.warps = [0 0]; | ||
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| % special maps | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.ct.native = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.ct.warped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.ct.dartel = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.pp.native = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.pp.warped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.pp.dartel = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.WMH.native = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.WMH.warped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.WMH.mod = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.WMH.dartel = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.SL.native = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.SL.warped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.SL.mod = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.SL.dartel = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.native = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.warped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.mod = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.dartel = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.atlas.native = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.atlas.warped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.atlas.dartel = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.label.native = 1; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.label.warped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.label.dartel = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.las.native = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.las.warped = 0; | ||
| matlabbatch{1}.spm.tools.cat.estwrite.output.las.dartel = 0; | ||
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| % ------------------------------------------------------------------------ | ||
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| %% smoothing | ||
| % ------------------------------------------------------------------------ | ||
| matlabbatch{2}.spm.spatial.smooth.fwhm = repmat(4,1,3); % smoothing filter size 4x4x4 | ||
| matlabbatch{2}.spm.spatial.smooth.dtype = 0; | ||
| matlabbatch{2}.spm.spatial.smooth.im = 0; | ||
| matlabbatch{2}.spm.spatial.smooth.prefix = 's4_'; | ||
| % ------------------------------------------------------------------------ | ||
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| %% | ||
| % Use to directly run script keep commented out if want to adapt using GUI | ||
| %spm_jobman('run',matlabbatch); |
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