What about trying:
fslchfiletype NIFTI badimage betterimage
Does that help?
All the best,
Mark
On 2 Jul 2009, at 14:50, Armin Biller wrote:
> Hi Mark,
>
> unfortunatelly, betterimage still does not work with FSLView...
>
> All the best,
> Armin
>
>
> 2009/7/2 Mark Jenkinson <[log in to unmask]>:
>> 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
>>>
>>
>
>
>
> --
> Dr. A. Biller
> Abteilung für Neuroradiologie
> Universität Heidelberg
> Im Neuenheimer Feld 400
> 69120 Heidelberg
>
|