Regarding the fslstats output, your usage is wrong. It should be `
fslstats .../DWI1_rescaled -R`.
The way you had it, fslstats is trying to read "-R" as an image, which is
why you get "failed to find header file for '-R'"
cheers,
Brian
> This means that the file is not complete - probably there's not as
> much data as the header claims there should be. So the program that
> created it had a problem, possibly because of RAM/swap issues for this
> big file (see the FAQ).
>
> Cheers.
>
>
> On 23 Feb 2010, at 18:49, Julio Duarte wrote:
>
>> I apply fslstats -R .../DWI1_rescaled and it throws:
>>
>> ** ERROR (nifti_image_read): failed to find header file for '-R'
>> ** ERROR: nifti_image_open(-R): bad header info
>> Error: failed to open file -R
>> ERROR: Could not open image -R
>> Image Exception : #22 :: Failed to read volume -R
>>
>> what does this mean?
>>
>> thanks,
>>
>> Julio
>> On Feb 23 2010, David Flitney wrote:
>>
>>> I make that roughly 10G in size? Are your computers 64bit? Although
>>> that's big there's no defined limit in fslview and I'm a little
>>> suspicious about the "bad header info" message. I wouldn't expect
>>> to see that if you're running out of RAM. What does "fslstats -R
>>> DWI1_rescaled" say?
>>>
>>> On 23 Feb 2010, at 17:25, Julio Duarte wrote:
>>>
>>>> Using flirt in command mode (no optimize: -applyxfm and use s-form:
>>>> -usesqform) I was able to align a big DWI image to its
>>>> corresponding T1
>>>> (higher resolution) image using the s-form info. However, the
>>>> generated
>>>> image cannot be read by FSLVIew, which throws the following error:
>>>> ** ERROR: nifti_image_open(.../fsl/data/DWI1/DWI1_rescaled): bad
>>>> header info
>>>> Error: failed to open file .../fsl/data/DWI1/DWI1_rescaled
>>>> terminate called after throwing an instance of 'Image::Exception'
>>>> what(): Failed to open file .../fsl/data/DWI1/DWI1_rescaled
>>>> .../fsl/bin/fslview: line 7: 898 Abort trap $
>>>> {FSLDIR}/bin/fslview.app/Contents/MacOS/fslview $@
>>>> (I added the "..." to avoid providing here the full path)
>>>> However, the header seems to be fine, as read by the nifti1_test and
>>>> fslcorrecthd utilities:
>>>> could it be its huge size??? I can load this image using slicer 3D
>>>> (although
>>>> it probably reads only the first volume). This happens on my
>>>> laptop and also
>>>> on a cluster. <nifti_image
>>>> nifti_type = 'NIFTI-1+'
>>>> header_filename =
>>>> '/Users/shirleymorillo/Desktop/fsl/data/DWI1_rescaled.nii.gz'
>>>> image_filename = '/Users/shirleymorillo/Desktop/fsl/data/
>>>> DWI1_rescaled.nii.gz'
>>>> image_offset = '352'
>>>> ndim = '4'
>>>> nx = '208'
>>>> ny = '256'
>>>> nz = '176'
>>>> nt = '301'
>>>> dx = '1'
>>>> dy = '1'
>>>> dz = '1'
>>>> dt = '1'
>>>> datatype = '16'
>>>> datatype_name = 'FLOAT32'
>>>> nvox = '2820866048'
>>>> nbyper = '4'
>>>> byteorder = 'LSB_FIRST'
>>>> scl_slope = '1'
>>>> scl_inter = '0'
>>>> xyz_units = '2'
>>>> xyz_units_name = 'mm'
>>>> time_units = '8'
>>>> time_units_name = 's'
>>>> descrip = 'FSL4.0'
>>>> qform_code = '1'
>>>> qform_code_name = 'Scanner Anat'
>>>> qto_xyz_matrix = '0 0 1 -90.4148 -1 0 -0 124.62 0 1 -0 -149.787 0
>>>> 0 0 1'
>>>> qto_ijk_matrix = '-0 -1 0 124.62 0 0 1 149.787 1 -0 -0 90.4148 0 0
>>>> 0 1'
>>>> quatern_b = '0.5'
>>>> quatern_c = '-0.5'
>>>> quatern_d = '-0.5'
>>>> qoffset_x = '-90.4148'
>>>> qoffset_y = '124.62'
>>>> qoffset_z = '-149.787'
>>>> qfac = '-1'
>>>> qform_i_orientation = 'Anterior-to-Posterior'
>>>> qform_j_orientation = 'Inferior-to-Superior'
>>>> qform_k_orientation = 'Left-to-Right'
>>>> sform_code = '1'
>>>> sform_code_name = 'Scanner Anat'
>>>> sto_xyz_matrix = '0 0 1 -90.4148 -1 0 0 124.62 0 1 0 -149.787 0 0
>>>> 0 1'
>>>> sto_ijk matrix = '-0 -1 -0 124.62 -0 -0 1 149.787 1 -0 -0 90.4148
>>>> 0 0 0 1'
>>>> sform_i_orientation = 'Anterior-to-Posterior'
>>>> sform_j_orientation = 'Inferior-to-Superior'
>>>> sform_k_orientation = 'Left-to-Right'
>>>> num_ext = '0'
>>>> />
>>>
>>>
>>
>
>
> ---------------------------------------------------------------------------
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> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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