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
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