Hi,
it's "ä, ü, ö" but "ß" will also cause troubles.
Cheers-
Andreas
________________________________________
Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Mark Jenkinson [[log in to unmask]]
Gesendet: Freitag, 3. Juli 2009 00:07
An: [log in to unmask]
Betreff: Re: [FSL] missing header/image file
Hi,
Not sure what a muted vowel is, but if it is a non-English character
then I can imagine that this might cause some problems. It isn't
something we've rigorously tested, so best thing is to be safe and
avoid it. What we do know is that spaces in filenames are very bad
and must be avoided!
Glad it is sorted out though.
All the best,
Mark
On 2 Jul 2009, at 19:27, Armin Biller wrote:
> Hi Mark,
>
> we've got it! With the filename containing muted vowels FSLView
> refused to open the image ;)
>
> Thank you very much!
>
> All the best,
> Armin
>
> 2009/7/2, Mark Jenkinson <[log in to unmask]>:
>> 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
>>>
>>>
>>
>
>
> --
> Dr. A. Biller
> Abteilung für Neuroradiologie
> Universität Heidelberg
> Im Neuenheimer Feld 400
> 69120 Heidelberg
>
