[pymvpa] mask_vt.nii.gz
jie zhang
zhang.33 at hotmail.com
Wed Jan 25 12:59:38 UTC 2012
Dear experts,
I was trying to follow the tutorial step by step, but got stuck because the scripts can not find the file named "mask_vt.nii.gz". I was using neurodebian, and I think I installed everything mentioned in the documentation. Could anybody please point out to me what I missed, or where I can download the tutorial dataset? many thanks!
Mike
here is the error message:
In [2]: ds = get_haxby2001_data()ERROR: An unexpected error occurred while tokenizing inputThe following traceback may be corrupted or invalidThe error message is: ('EOF in multi-line statement', (96, 0))
---------------------------------------------------------------------------IOError Traceback (most recent call last)
/usr/share/pyshared/mvpa/<ipython console> in <module>()
/usr/lib/pymodules/python2.6/mvpa2/tutorial_suite.pyc in get_haxby2001_data(path, roi) 40 def get_haxby2001_data(path=None, roi='vt'): 41 if path is None:---> 42 ds = get_raw_haxby2001_data(roi=roi) 43 else: 44 ds = get_raw_haxby2001_data(path, roi=roi)
/usr/lib/pymodules/python2.6/mvpa2/tutorial_suite.pyc in get_raw_haxby2001_data(path, roi) 35 return ds 36 else:---> 37 return load_datadb_tutorial_data(path=path, roi=roi) 38 39
/usr/lib/pymodules/python2.6/mvpa2/misc/data_generators.pyc in load_datadb_tutorial_data(path, roi) 377 ds = fmri_dataset(samples=os.path.join(path, 'bold.nii.gz'), 378 targets=attr.targets, chunks=attr.chunks,--> 379 mask=mask) 380 return ds 381
/usr/lib/pymodules/python2.6/mvpa2/datasets/mri.pyc in fmri_dataset(samples, targets, chunks, mask, sprefix, tprefix, add_fa) 204 # figure out what the mask is, but only handle known cases, the rest
205 # goes directly into the mapper which maybe knows more
--> 206 maskimg = _load_anyimg(mask) 207 if maskimg is None: 208 pass
/usr/lib/pymodules/python2.6/mvpa2/datasets/mri.pyc in _load_anyimg(src, ensure, enforce_dim) 335 # try opening the beast; this might yield none in case of an unsupported
336 # argument and is handled accordingly below
--> 337 data = _img2data(src) 338 if not data is None: 339 imgdata, imghdr, imgtype = data
/usr/lib/pymodules/python2.6/mvpa2/datasets/mri.pyc in _img2data(src) 58 if isinstance(src, str): 59 # filename
---> 60 img = nibabel.load(src) 61 else: 62 # assume this is an image already
/usr/lib/pymodules/python2.6/nibabel/loadsave.pyc in load(filename) 51 else: 52 klass = spm2.Spm2AnalyzeImage---> 53 return klass.from_filename(filename) 54 55
/usr/lib/pymodules/python2.6/nibabel/spatialimages.pyc in from_filename(klass, filename) 395 def from_filename(klass, filename): 396 file_map = klass.filespec_to_file_map(filename)--> 397 return klass.from_file_map(file_map) 398 399 @classmethod
/usr/lib/pymodules/python2.6/nibabel/analyze.pyc in from_file_map(klass, file_map) 1303 ''' 1304 hdr_fh, img_fh = klass._get_fileholders(file_map)-> 1305 hdrf = hdr_fh.get_prepare_fileobj(mode='rb') 1306 header = klass.header_class.from_fileobj(hdrf) 1307 if hdr_fh.fileobj is None: # was filename
/usr/lib/pymodules/python2.6/nibabel/fileholders.pyc in get_prepare_fileobj(self, *args, **kwargs) 67 obj.seek(self.pos) 68 elif self.filename is not None:---> 69 obj = allopen(self.filename, *args, **kwargs) 70 if self.pos != 0: 71 obj.seek(self.pos)
/usr/lib/pymodules/python2.6/nibabel/volumeutils.pyc in allopen(fname, *args, **kwargs) 847 else: 848 opener = open--> 849 return opener(fname, *args, **kwargs) 850 851
/usr/lib/python2.6/gzip.pyc in open(filename, mode, compresslevel) 31 32 """---> 33 return GzipFile(filename, mode, compresslevel) 34 35 class GzipFile:
/usr/lib/python2.6/gzip.pyc in __init__(self, filename, mode, compresslevel, fileobj) 77 mode += 'b' 78 if fileobj is None:---> 79 fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb') 80 if filename is None: 81 if hasattr(fileobj, 'name'): filename = fileobj.name
IOError: [Errno 2] No such file or directory: './data/mask_vt.nii.gz'
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