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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