Hi,
This looks absolutely fine to me.
What happens if you run a bad image once through
fslmaths. That is:
fslmaths badimage betterimage
Does betterimage work fine with FSLView?
All the best,
Mark
On 2 Jul 2009, at 13:47, Armin Biller wrote:
> Hi Mark,
>
> all images were assessed by a 3T Siemens Tim Trio. They were converted
> from DICOM to FSLNifti (dual-file) by Jolindas MRIConvert. However,
> MRIConvert runs on MS Vista whereas FSL's enviorement is VMWare.
> Please find the fslhd output of an exemplary file below.
> Again, thanks a lot.
>
> All the best,
> Armin
>
> Output of fslhd:
> filename frki.hdr
>
> sizeof_hdr 348
> data_type INT16
> dim0 3
> dim1 240
> dim2 256
> dim3 160
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units Unknown
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 1.0000000000
> pixdim2 1.0000000000
> pixdim3 0.9998550415
> pixdim4 0.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 0
> cal_max 0.0000
> cal_min 0.0000
> scl_slope 1.000000
> scl_inter 0.000000
> phase_dim 1
> freq_dim 2
> slice_dim 3
> slice_name alternating_increasing
> slice_code 3
> slice_start 0
> slice_end 159
> slice_duration 356.762512
> time_offset 0.000000
> intent Unknown
> intent_code 0
> intent_name
> intent_p1 0.000000
> intent_p2 0.000000
> intent_p3 0.000000
> qform_name Scanner Anat
> qform_code 1
> qto_xyz:1 -0.024646 0.022456 0.999299 -80.448250
> qto_xyz:2 -0.999696 -0.000501 -0.024638 158.360138
> qto_xyz:3 0.000052 0.999748 -0.022458 -184.505615
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Anterior-to-Posterior
> qform_yorient Inferior-to-Superior
> qform_zorient Left-to-Right
> sform_name Unknown
> sform_code 0
> sto_xyz:1 0.000000 0.000000 0.000000 0.000000
> sto_xyz:2 0.000000 0.000000 0.000000 0.000000
> sto_xyz:3 0.000000 0.000000 0.000000 0.000000
> sto_xyz:4 0.000000 0.000000 0.000000 0.000000
> sform_xorient Unknown
> sform_yorient Unknown
> sform_zorient Unknown
> file_type NIFTI-1
> file_code 2
> descrip MPRAGE_p2
> aux_file
>
>
>
>
>
> 2009/7/2 Mark Jenkinson <[log in to unmask]>:
>> Hi,
>>
>> The cal_min and cal_max are not important, although space
>> for them must exist in the header according to the standard.
>> Are these images in nifti or analyze format? And are they
>> a single-file nifti or dual-file? What is the output of fslhd?
>> How did you get these images? Were they converted by
>> yourself from DICOM or some other format? If so, how?
>>
>> This is certainly a puzzling and serious problem, but
>> hopefully answers to the questions above will help us track
>> down the problem.
>>
>> All the best,
>> Mark
>>
>>
>> On 2 Jul 2009, at 13:13, Armin Biller wrote:
>>
>>> Hi,
>>>
>>> some files of my data set can not be opened by FSLView ("Missing
>>> header/image file"). The data set contains (anatomical as well as
>>> functional)
>>> image files of 18 subjects of which 8 can not be opend (regardless
>>> of the
>>> MR
>>> sequence saved). Files of the remaining 10 subjects can be
>>> displayed in
>>> FSLView. Interestingly, BET and fslmaths work fine with all files.
>>> There
>>> are no
>>> differences in data acquisition. Files that fail to open in
>>> FLSView lack
>>> the
>>> cat_min / cat_max entry of the header. However, neither manual nor
>>> automatic header correction ("correctheader") worked.
>>>
>>> Any ideas? Thank you!
>>>
>>> All the best,
>>> Armin
>>>
>>
>
>
>
> --
> Dr. A. Biller
> Abteilung für Neuroradiologie
> Universität Heidelberg
> Im Neuenheimer Feld 400
> 69120 Heidelberg
>
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