[Neuroimaging] FmriRealign4D: how to make it write files?
katiesurrence at gmail.com
Fri Sep 18 20:13:24 CEST 2015
I asked this question on neurostars, but haven't received a reply, so I
thought I'd try here.
When I run a program containing this code snippet:
for sub in subjects.keys():
for run in subjects[sub]:
infile = os.path.join(root, sub, 'func', run, '4D.nii')
realigner = FmriRealign4d()
realigner.inputs.in_file = [infile]
realigner.inputs.tr = 2.2
realigner.inputs.slice_order = range(0, 34, 2) + range(1, 35, 2)
realigner.inputs.time_interp = True
outfile = os.path.join(root, sub, 'func', run, 'ra4D.nii')
f = open(outfile, 'w')
realigner._out_file = [outfile]
parfile = os.path.join(root, sub, 'func', run, 'motpar.txt')
p = open(parfile, 'w')
realigner._par_file = [parfile]
res = realigner.run()
I get a bunch of output to the console to indicate realignment/slice timing
is happening, but the only changes on disk are that my files are created.
They remain at zero bytes. (Specifying the _out_file and _par_file
attributes and making empty versions of the files were things I tried to
coax it into writing files. My original version did neither of these things
and had the same problem.)
I appreciate any help you can provide.
Katie Surrence, M.S.
Social Cognition Laboratory
New York State Psychiatric Institute
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Neuroimaging