wtclarke
commented
3 years ago Hi @benhibou ,
Sorry for the delay in replying to your message. Could you describe the data a bit more? What other dimensions (coils, repeats, other encodings) are you expecting?
BW
Will
Hello,
I have try to use spec2nii with Bruker data but it quickly run into trouble as it try to reshape some array:
I issue the command --> spec2nii bruker -m FID -o ./ ./10/fid while I reside into a directory which contains a subdirectory "./10". In ./10 is the "method" file and all the relevant fid, ... as they appear when a MRS experiment is run with Bruker. The output gives:
Traceback (most recent call last): File "/Users/benagain/opt/anaconda3/bin/spec2nii", line 10, in
sys.exit(main())
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/spec2nii/spec2nii.py", line 485, in main
spec2nii(args)
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/spec2nii/spec2nii.py", line 247, in init
args.func(args)
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/spec2nii/spec2nii.py", line 456, in bruker
self.imageOut, self.fileoutNames = read_bruker(args)
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/spec2nii/bruker.py", line 42, in read_bruker
for data, orientation, dwelltime, meta, name in yield_bruker(args):
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/spec2nii/bruker.py", line 71, in yield_bruker
d = Dataset(args.file, property_files=[bruker_properties_path], parameter_files=['method'])
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/brukerapi/dataset.py", line 180, in init
self.load()
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/brukerapi/dataset.py", line 254, in load
self.load_data()
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/brukerapi/dataset.py", line 502, in load_data
self._data = self._read_data()
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/brukerapi/dataset.py", line 512, in _read_data
return self._schema.deserialize(data, self._schema.layouts)
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/brukerapi/schemas.py", line 162, in deserialize
data = self._acquisitions_to_encode(data, layouts)
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/brukerapi/schemas.py", line 200, in _acquisitions_to_encode
return np.reshape(data, layouts['encoding_space'], order='F')
File "<__array_function__ internals>", line 6, in reshape
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 301, in reshape
return _wrapfunc(a, 'reshape', newshape, order=order)
File "/Users/benagain/opt/anaconda3/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 61, in _wrapfunc
return bound(args, **kwds)
ValueError: cannot reshape array of size 8192 into shape (2048,1)
In the experiment the parameter PVM_SpecMatrix corresponds to a 1-dimensional array and is equal to 2048. I am not sure if this could be connected to the last line of the error message.
Thank you in advance for your comment,
Benoit