Detects echo time in FID sidecar file

fsl_mrs/scripts/fsl_mrs

@@ -295,6 +295,8 @@ def main():
     # Echo time
     if args.TE is not None:
         echotime = args.TE*1E-3
+    elif 'TE' in dataheader:
+        echotime = dataheader['TE']
     elif 'meta' in basisheader:
         if 'TE' in basisheader['meta']:
             echotime = basisheader['meta']['TE']
@@ -306,6 +308,8 @@ def main():
         echotime = None
     # Internal and Water quantification if requested
     if (mrs.H2O is None) or (echotime is None):
+        if echotime is None:
+            warnings.warn('H2O file provided but could not determine TE: no absolute quantification will be performed.',UserWarning)
         res.calculateConcScaling(mrs,referenceMetab=args.internal_ref)
     elif args.tissue_frac is None:
         res.calculateConcScaling(mrs,

fsl_mrs/utils/mrs_io/fsl_io.py

@@ -43,7 +43,9 @@ def readNIFTI(datafile,squeezeSVS=True):
                 'json':jsonParams,
                 'centralFrequency':jsonParams['ImagingFrequency'],
                 'dwelltime':jsonParams['Dwelltime'],
-                'bandwidth':1/jsonParams['Dwelltime']}
+                 'bandwidth':1/jsonParams['Dwelltime']}
+        if "EchoTime" in jsonParams:
+            header['TE'] = jsonParams['EchoTime']
 
     # If there is only one FID (SVS) and squeezeSVS is true then
     # remove singleton dimensions
@@ -212,4 +214,4 @@ def readAndGenFSLBasis(file,readoutShift,bandwidth,points):
                     'dwelltime':1/bandwidth,
                     'fwhm':lw}
 
-    return FID, metabo, header
\ No newline at end of file
+    return FID, metabo, header