[Neuroimaging] load data and get negative dim in header

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Hello,


I use "preproc-sess" command of Freesurfer to to project my func data to individual anatomy space,


preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh -fwhm 0 -per-run -force


and I try to load nifti data with "get_data()" of nibabel, but it could not work, error info is here:


>>> f.get_data()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line 341, in get_data
    return np.asanyarray(self._data)
  File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line 512, in asanyarray
    return array(a, dtype, copy=False, order=order, subok=True)
  File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 55, in __array__
    self._data = self._read_data()
  File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 60, in _read_data
    data = self.header.data_from_fileobj(fileobj)
  File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 486, in data_from_fileobj
    data = self.raw_data_from_fileobj(fileobj)
  File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 458, in raw_data_from_fileobj
    return array_from_file(shape, dtype, fileobj, offset)
  File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py", line 493, in array_from_file
    raise IOError(msg)
IOError: Expected -1804 bytes, got 264809160 bytes from file "fmcpr.vol2surf.lh.nii.gz"
 - could the file be damaged?


Then I check the header, and I mark the negative value in "dim" of the header:

>>> print(f.get_header())

<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'

sizeof_hdr      : 348

data_type       :

db_name         :

extents         : 0

session_error   : 0

regular         :

dim_info        : 0

dim             : [  4  -1   1   1 451   1   1   1]

intent_p1       : 0.0

intent_p2       : 0.0

intent_p3       : 0.0

intent_code     : none

datatype        : float32

bitpix          : 32

slice_start     : 0

pixdim          : [-1.          1.          1.          1.          2.00000072  1.          1.

  1.        ]

vox_offset      : 352.0

scl_slope       : 0.0

scl_inter       : 0.0

slice_end       : 0

slice_code      : unknown

xyzt_units      : 10

cal_max         : 0.0

cal_min         : 0.0

slice_duration  : 0.0

toffset         : 0.0

glmax           : 0

glmin           : 146790

descrip         : FreeSurfer May 13 2013

aux_file        :

qform_code      : scanner

sform_code      : scanner

quatern_b       : -0.0115927606821

quatern_c       : -0.996071338654

quatern_d       : -0.0864994972944

qoffset_x       : 73344.5546875

qoffset_y       : -1492.14978027

qoffset_z       : -2311.28955078

srow_x          : [ -9.99280393e-01   2.56918129e-02   2.79041883e-02   7.33445547e+04]

srow_y          : [  2.04970520e-02   9.84766901e-01  -1.72667429e-01  -1.49214978e+03]

srow_z          : [  3.19152586e-02   1.71971247e-01   9.84584868e-01  -2.31128955e+03]

intent_name     :

magic           : n+1



Well, I have tried to connect Freesurfer mailing list, but there may be something wrong with my e-mail address,


and it would be helpful to me if you tell me why there is an negative value in the header or how can I fix it.


Thanks in advance,


Bai Haohao




Version info:
System: ubuntu-16.04.1-server-amd64
Freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
nibabel: python-nibabel  1.2.2-1
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