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README.md

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-# Displasias
-Concatenación Código Displasias 
+# ratCortex-dMRIstreams
+
+Code to process dMRI volumes and create cortical streamlines in rat data. :information_source: [**Info & details**](https://hackmd.io/@servindc/ratCortex-dMRI)
+
+## Setup
+
+1. Install the [MINC](https://en.wikibooks.org/wiki/MINC) tools required for the code:
+    ```bash
+    sudo apt install minc-tools
+    ```
+
+2. Create a conda environment:
+    ```bash
+    conda env create --file environment.yml
+    ```
+
+3. Activate the environment:
+    ```bash
+    conda activate cx-streams-env
+    ```
+
+4. Display script help:
+    ```bash
+    nii2streams.sh -h
+    ```

environment.yml

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+# run: conda env create --file environment.yml
+name: cx-streams-env
+channels:
+ - conda-forge
+ - anaconda
+ - mrtrix3
+dependencies:
+ - python
+ - matplotlib
+ - numpy
+ - nibabel
+ - dipy
+ - networkx
+ - scipy
+ - scikit-image
+ - scikit-learn
+ - mrtrix3

get_seeds.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Adjust seed line
+
+@author: dcortex
+"""
+from os.path import join, basename
+from os import chdir
+import numpy as np
+import nibabel as nib
+from sklearn.neighbors import NearestNeighbors
+import networkx as nx
+from scipy.interpolate import splprep, splev
+
+def sort_points(seeds):
+    """
+    Returns sorted 'seeds' (np.ndarray) by their nearest neighbors
+    """
+    if len(seeds)==0: return np.array([])
+    clf = NearestNeighbors(n_neighbors=2).fit(seeds)
+    G = clf.kneighbors_graph()  # sparse N x N matrix
+
+    T = nx.from_scipy_sparse_matrix(G)
+
+    paths = [list(nx.dfs_preorder_nodes(T, i)) for i in range(len(seeds))]
+
+    mindist = np.inf
+    minidx = 0
+
+    for i in range(len(seeds)):
+        p = paths[i]           # order of nodes
+        ordered = seeds[p]    # ordered nodes
+        # find cost of that order by the sum of euclidean distances between points (i) and (i+1)
+        cost = (((ordered[:-1] - ordered[1:])**2).sum(1)).sum()
+        if cost < mindist:
+            mindist = cost
+            minidx = i
+    seeds = seeds[paths[minidx]]
+    # Medial a lateral
+    if seeds[0][1] < seeds[-1][1]: seeds = seeds[::-1]
+    return seeds
+
+def smooth_curve(x, y, s=0.5):
+    tck, u = splprep([x, y], s=s)
+    smooth_points = np.array(splev(u, tck)).T
+    return smooth_points
+
+def get_seeds_from_nii(f_name, subject, side='l', smooth=False, save=True, s=0.1, 
+                        save_folder='~/Descargas',):
+    lines_volume = nib.load(f_name).get_fdata()
+
+    seeds_dict = {}
+    for slice_n in range(10,16):
+
+        sx, sy = np.array(np.nonzero(lines_volume[:,:,slice_n]))
+        seeds = np.array([sx,sy]).T
+
+        if len(seeds)==0: continue
+
+        seeds = sort_points(seeds)
+        if smooth: seeds = smooth_curve(*seeds.T, s=s)
+
+        # Add z coordinate
+        ones = np.ones([len(seeds), 1])
+        seeds = np.concatenate((seeds, slice_n*ones), axis=1)[1:,:] 
+        #               remove first entry because of reasons ^
+
+        if save:
+            seeds_name = f'{subject}_{side}_{slice_n}_seeds'
+            if smooth: seeds_name += '_smooth'
+
+            np.savetxt(join(save_folder, basename(seeds_name)+'.txt'), seeds)
+            print(f'\n  Created file: {basename(seeds_name)}.txt in: {save_folder}')      
+
+        seeds_dict[seeds_name] = seeds
+
+    return seeds_dict
+
+#_____________________________________________________________________________    
+
+
+if __name__ == "__main__":
+    import sys
+    import subprocess
+    from os.path import dirname
+
+    #subject = sys.argv[1] # subject = '37A
+    #side = 'l'
+
+    #f_name = f'minc/{subject}_{side}_outline.nii' 
+    f_name = sys.argv[1]
+    out_dir = sys.argv[2]
+    prefix = sys.argv[3]
+    try:
+        n_seeds = sys.argv[4]
+    except IndexError:
+        n_seeds = 150
+    print(f'\n  Using {n_seeds} seeds')
+
+    #subject = basename(f_name).split('_')[0]
+    side = basename(f_name).split('_')[1]
+    seeds = get_seeds_from_nii(f_name, subject=prefix, side=side, smooth=True, save=True,
+                               s=10, save_folder=out_dir, )
+
+    #out_dir = dirname(f_name)
+    for seeds_name in list(seeds.keys()):
+
+        convert1 = (f"tckconvert {join(out_dir, seeds_name)}.txt"
+                    f" {join(out_dir, seeds_name)}.tck ") 
+        # -voxel2scanner ../{subject}_x2.nii 
+        resample = (f"tckresample -num_points {n_seeds} -nthreads 0"
+                    f" {join(out_dir, seeds_name)}.tck"
+                    f" {join(out_dir, seeds_name)}_resampled.tck")
+        convert2 = (f"tckconvert {join(out_dir, seeds_name)}_resampled.tck"
+                    f" {join(out_dir, seeds_name)}_resampled_[].txt")
+        rename = (f"mv {join(out_dir, seeds_name)}_resampled_0000000.txt"
+                  f" {join(out_dir, seeds_name)}_resampled.txt")
+        for my_command in [convert1, resample, convert2, rename]:
+            process = subprocess.Popen(my_command.split(), stdout=subprocess.PIPE)
+            output, error = process.communicate()
+
+        print((f"\n  Created file: {join(out_dir, seeds_name)}_resampled"
+               f"(txt & tck) in: {out_dir}\n"))
+
+#!tckconvert {seeds_name}.txt {seeds_name}.tck -voxel2scanner ../{subject}_x2.nii
+#!tckresample -num_points 150 -nthreads 0 {seeds_name}.tck {seeds_name}_resampled.tck
+#!tckconvert {seeds_name}_resampled.tck {seeds_name}_resampled_[].txt
+
+    sys.exit()
+
+
+
+
+
+
+
+

make_grid.sh

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+#!/bin/bash
+
+if [ "$1" == "-h" -o "$1" == "--help" -o "$1" == "" ]; then
+  echo -e "\n	Usage: `basename $0` grid_in grid_mid [output_path]"
+  echo -e "\n	Computes grid for the mincLaplace script."
+  echo -e "\n	Returns '_grid_123.nii.gz' & '_grid_123.mnc'.\n"
+  exit 0
+fi
+
+grid_in=$1
+grid_mid=$2
+out_folder=${3:-$(dirname $grid_in)}
+
+echo -e "\n 	Making new grid in: '$out_folder'" # -e enables interpretation of backslash escapes
+echo -e "\n 	Using: '$grid_in' & '$grid_mid'\n" 
+
+# Area's default values:
+in0=${4:-1}
+mid=${5:-2}
+out=${6:-3}
+
+gridsufix=grid_${in0}${mid}${out}
+grid_name=$(basename ${grid_in%_grid_in*})	# e.g. 37A_l
+
+#echo $out_folder/${grid_name}_${gridsufix}.nii.gz
+
+#for side in  l #r 	# left right
+
+#grid_in=$(find $out_folder -type f -iname "*_${side}_grid_in.nii.gz")
+#grid_mid=$(find $out_folder -type f -iname "*_${side}_grid_mid.nii.gz")
+
+#rat_id=$(basename ${grid_in%%_*})
+
+#if [ -f "${out_folder}/${rat_id}_${side}_${gridsufix}.nii.gz" ]
+#then
+#	echo -e "\n		Archivo '${rat_id}_${side}_${gridsufix}.nii.gz' ya existe.\n\n"
+
+#elif [ -f "${rat_id}_${side}_grid_in.nii.gz" -a -f "${rat_id}_${side}_grid_mid.nii.gz" ]
+#elif [ -f $grid_in -a -f $grid_mid ]
+
+if [ -f "$out_folder/${grid_name}_${gridsufix}.nii.gz" ]
+then
+	echo -e "\n		File '${grid_name}_${gridsufix}.nii.gz' already exists.\n"
+elif [ -f $grid_in -a -f $grid_mid ]
+then
+	#mrcalc ${rat_id}_${side}_grid_in.nii.gz 0 -mult $out -add base.nii
+	mrcalc $grid_in 0 -mult $out -add ${out_folder}/base.nii
+
+	mid_scalar="$(($mid-$out))"
+	#mrcalc ${rat_id}_${side}_grid_mid.nii.gz $mid_scalar -mult base2.nii
+	mrcalc $grid_mid $mid_scalar -mult ${out_folder}/base2.nii
+
+	in_scalar="$(($in0-$out))"
+	#mrcalc ${rat_id}_${side}_grid_in.nii.gz $in_scalar -mult base3.nii
+	mrcalc $grid_in $in_scalar -mult ${out_folder}/base3.nii
+
+	#mrcalc ${rat_id}_${side}_grid_in.nii.gz ${rat_id}_${side}_grid_mid.nii.gz -min $mid -mult base4.nii
+	mrcalc $grid_in $grid_mid -min $mid -mult ${out_folder}/base4.nii
+
+	#mrcalc base.nii base2.nii -add base3.nii -add base4.nii -add "${rat_id}_${side}_grid_${in0}${mid}${out}.nii.gz"
+	a=${out_folder}/base.nii; b=${out_folder}/base2.nii
+	c=${out_folder}/base3.nii; d=${out_folder}/base4.nii
+	#mrcalc  $a $b -add $c -add $d -add ${out_folder}/${rat_id}_${side}_${gridsufix}.nii.gz
+	mrcalc  $a $b -add $c -add $d -add $out_folder/${grid_name}_${gridsufix}.nii.gz
+
+	gio trash ${out_folder}/base*.nii
+
+	#nii2mnc ${out_folder}/${rat_id}_${side}_${gridsufix}.nii.gz ${out_folder}/${rat_id}_${side}_${gridsufix}.mnc
+	nii2mnc $out_folder/${grid_name}_${gridsufix}.nii.gz $out_folder/${grid_name}_${gridsufix}.mnc
+
+	echo -e "\n Grids '$out_folder/${grid_name}_${gridsufix}' (.mnc & .nii.gz) created in '$out_folder'\n"
+else
+	echo -e "\n	Error: files '$grid_in', '$grid_mid' missing.\n"
+fi
+
+