[Neuroimaging] Fwd: [Freesurfer] negative header after preproc-sess
Christopher Markiewicz
effigies at bu.edu
Thu Jul 27 11:59:41 EDT 2017
I agree with this viewpoint from a user/standards perspective. AFAIK only
FreeSurfer and nibabel support the surface hacks, and both also support the
.mgh format, so there's no real advantage to using NIfTI here. For
interoperability, other formats are more appropriate. I also think it's
reasonable to encourage FreeSurfer to move toward writing NIfTI-2 when
hacks are necessary to generate NIfTI-1 files.
>From a nibabel-as-multitool perspective, while I understand the concern
about propagating broken formats, I also think we should be able to read
images as created by existing packages, as long as doing so doesn't harm
our ability to read standard-conforming files.
Chris
On Thu, Jul 27, 2017 at 10:18 AM, Reynolds, Richard C. (NIH/NIMH) [E] <
reynoldr at mail.nih.gov> wrote:
> 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>
> Date: Thu, Jul 6, 2017 at 7:07 AM
> Subject: Re: [Freesurfer] negative header after preproc-sess
> To: 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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>
>
>
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