Added report

spinal_dmri_pipeline/scripts/fwdti.py

+#!/usr/bin/env python
+
+# Simple script for fitting Free-water eliminated DTI using DIPY
+
+# Author: S. Jbabdi - 02/2022
+
+import argparse
+
+p = argparse.ArgumentParser("Fit FOD")
+p.add_argument('--data',required=True,type=str,
+                metavar='<IMAGE>',help='input DWI data')
+p.add_argument('--bvecs',required=True,type=str,
+                metavar='<FILE>',help='bvecs ASCII text file')
+p.add_argument('--bvals',required=True,type=str,
+                metavar='<FILE>',help='bvals ASCII text file')
+p.add_argument('--out',required=True,type=str,
+                metavar='<str>',help='output basename')
+p.add_argument('--mask',required=True,type=str,
+                metavar='<IMAGE>',help='brain mask')
+p.add_argument('--verbose',action="store_true",
+                help='print info')
+
+
+# Parse Arguments here
+args = p.parse_args()
+
+# ------------ Other imports
+import numpy as np
+from fsl.data.image import Image
+
+# ----- dipy imports ------ #
+import dipy.reconst.fwdti as fwdti
+from dipy.core.gradients import gradient_table
+
+
+# --- Start here
+# Get data
+if args.verbose:
+    print('Read data')
+data   = Image(args.data)
+header = data.header # store header info
+data   = data.data   # get data array
+# Brain mask
+mask = Image(args.mask).data
+# bvals, bvecs text to array
+bvals = np.loadtxt(args.bvals)
+bvecs = np.loadtxt(args.bvecs).T
+bvecs[bvals<5] = [1,0,0] # fix in case bvecs=0,0,0
+bvecs = bvecs / np.sqrt(np.sum(bvecs**2,axis=1,keepdims=True)) # normalise
+
+
+# Set gradient table
+gtab = gradient_table(bvals, bvecs)
+
+
+# Fit ODF model
+if args.verbose:
+    print('Fit model')
+
+fwdtimodel = fwdti.FreeWaterTensorModel(gtab)
+fwdtifit   = fwdtimodel.fit(data, mask=mask)
+
+
+if args.verbose:
+    print('Save output')
+
+outputlist = ['FA','AD','MD','MODE','RD','SPHERICITY','LINEARITY','PLANARITY','F']
+for o in outputlist:
+    img = Image(getattr(fwdtifit,o.lower()),header=header)
+    img.save(f'{args.out}_{o}')
+
+
+if args.verbose:
+    print('Done')
+
+
+
+