When the nifti standard was adopted, they used a short int to represent
the dimensions. Unfortunately, this only allows for a maximum dimension
of 32k, which is not big enough for surfaces. So I hacked the FS nifti
format to put a -1 as the first dim at which point the FS code will go
to another place in the header to get the spatial dimensions. It is
possible to reshape the spatial dimensions as long as the largest prime
factor is less than 32k (see mri_surf2surf with --reshape option). Other
than that, you might ask the nibabel people to program the same hack.
On 6/25/17 6:48 AM, Bai Haohao wrote:
Hello Freesurfer experts,
I am running my data with preproc-sess to project my func data to
individual anatomy file, and the command shows as below:
preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh -fwhm
0 -per-run -force
And the subjectname point to the subject dir that created after recon-all.
After the running completed, I try to load data from
fmcpr.sm0.self.lh.nii.gz with nibabel, and I get this error info:
>>> 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 file header by nibabel, and I get this:
>>> 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
Note that the dim has value -1, but when I use -surface fsaverage, the
dim is correct(show as below):
dim : [ 4 27307 1 6 451 1 1 1]
And I read the source code, the difference between self and fsaverage
is appeared when running rawfunc2surf-sess, and log files are attached.
I have tried many commands to load data from fmcpr.sm0.self.lh.nii.gz,
such as fslview, freeview, mri_convert, mri_surf2surf, ...
and only tksurfer could read this file by -timecourse
fmcpr.sm0.self.lh.nii.gz.
I want to figure out how could I fix it, and any suggestion would be
helpful.
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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