[Neuroimaging] Fwd: [Freesurfer] negative header after preproc-sess
Reynolds, Richard C. (NIH/NIMH) [E]
reynoldr at mail.nih.gov
Thu Jul 27 10:18:06 EDT 2017
This seems like an appropriate case to be using the
NIFTI-2 standard, which uses 64-bit values rather than
the 16-bits for NIFTI-1 (which was done just to keep it
similar to ANALYZE).
For that matter, GIFTI was made to be the surface
alternative to NIFTI, and FreeSurfer supports it, as does
nibabel, it seems.
Even without those options, it seems like FreeSurfer
can still output what you want in a useful format.
Breaking the NIFTI-1 standard is causing you trouble.
Maybe propagating that is not necessary.
- rick
________________________________
From: Bai Haohao <jarblank1200 at gmail.com>
Sent: Thursday, July 27, 2017 9:41:13 AM
To: neuroimaging at python.org
Subject: [Neuroimaging] Fwd: [Freesurfer] negative header after preproc-sess
Dear nibabel experts,
I forward this email to nibabel mailing list because I think it is related to nibabel, even this problem is caused by nifti standard and freesurfer.
I am using nibabel to load data after freesurfer "preproc-sess -suface self" and I get negative dim(-1 1 1, see origin email for detail), which makes nibabel.get_data() failed, but freesurfer first level analysis can be done successfully, in my view it means freesurfer can get data from this bad header.
I find a way to solve it is by using "mri_convert *.nii.gz *.mgz", then nibabel could get data from *.mgz. But I think if nibabel could support getting data from negative header file would be more helpful.
Just some undevelopped thoughts, I hope I express it clearly.
Best,
Bai Haohao
---------- Forwarded message ----------
From: Douglas Greve <greve at nmr.mgh.harvard.edu<mailto:greve at nmr.mgh.harvard.edu>>
Date: Thu, Jul 6, 2017 at 7:07 AM
Subject: Re: [Freesurfer] negative header after preproc-sess
To: freesurfer at nmr.mgh.harvard.edu<mailto:freesurfer at nmr.mgh.harvard.edu>
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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