This may just be a display range issue in FSLView (trying changing
the display range) or it may be that you lost all your data when you
converted to 16SI - you may need to scale/shift the values to a
sensible range before converting.
What does avwstats++ <image> -r -R give?
Cheers.
On 23 Oct 2006, at 21:35, =?ISO-8859-1?Q?Kelly?= wrote:
> Thanks for the input. I applied the tbss_1_preproc script to my
> image an
> d
> it did change the image to a 16-bit signed integer with positive voxel
> dimensions. However, when I load the new image into FSLview
> nothing show
> s
> up. I have added the avwhd output for the new file as well as the
> old ni
> fti
> image, is there something I am missing? Thanks!
>
> my script:
>
> remove_ext /home/kelly/t1mas.nii.gz`
> #echo processing /home/kelly/t1mas.nii.gz`
> avwhd -x /home/kelly/t1mas.nii.gz | sed "s/sform_code .*/sform_code =
> \'0\'/g" | sed "s/qform_code .*/qform_code = \'0\'/g" > grot.xml
> avwcreatehd grot.xml /home/kelly/t1mas_FAi.hdr
> /bin/rm grot.xml
>
> avwmaths_16SI /home/kelly/t1mas_FAi.hdr -ero /home/kelly/t1mas_FAi.hdr
>
> AVWHD
> filename t1mas_FAi.hdr
>
> sizeof_hdr 348
> data_type
> db_name
> extents 0
> session_error 0
> regular r
> hkey_un0
> dim0 3
> dim1 256
> dim2 256
> dim3 154
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units
> cal_units
> unused1 0
> datatype 4
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 0.9375000000
> pixdim2 0.9375000000
> pixdim3 0.9375000000
> pixdim4 1.0000000000
> pixdim5 1.0000000000
> pixdim6 1.0000000000
> pixdim7 1.0000000000
> vox_offset 0.0000
> funused1 1.0000
> funused2 0.0000
> funused3 0.0000
> cal_max 0.0000
> cal_min -32768.0000
> compressed 0
> verified 0
> glmax 0
> glmin 0
> descrip FSL3.3
> aux_file
> orient 0
> originator
> origin1 0
> origin2 0
> origin3 0
> generated
> scannum
> patient_id
> exp_date
> exp_time
> hist_un0
> views 0
> vols_added 0
> start_field 0
> field_skip 0
> omax 0
> omin 0
> smin 0
> smin 0
> file_type ANALYZE-7.5
> file_code 0
> [root@localhost kelly]# avwhd t1mas.nii.gz
> filename t1mas.nii.gz
>
> sizeof_hdr 348
> data_type FLOAT32
> dim0 3
> dim1 256
> dim2 256
> dim3 154
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 0.9375000000
> pixdim2 0.9375000000
> pixdim3 0.9375000000
> pixdim4 1.0000000000
> pixdim5 1.0000000000
> pixdim6 1.0000000000
> pixdim7 1.0000000000
> vox_offset 352
> cal_max 0.0000
> cal_min 0.0000
> scl_slope 1.000000
> scl_inter 0.000000
> phase_dim 0
> freq_dim 0
> slice_dim 0
> slice_name Unknown
> slice_code 0
> slice_start 0
> slice_end 0
> slice_duration 0.000000
> 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 -0.936773 0.036516 0.005412 118.365860
> qto_xyz:2 0.035667 0.930767 -0.106332 -98.821541
> qto_xyz:3 0.009515 0.106044 0.931435 -49.327732
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Posterior-to-Anterior
> qform_zorient Inferior-to-Superior
> sform_name Scanner Anat
> sform_code 1
> sto_xyz:1 -0.936773 0.036516 0.005407 118.365860
> sto_xyz:2 0.035668 0.930767 -0.106333 -98.821541
> sto_xyz:3 0.009510 0.106044 0.931435 -49.327732
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Posterior-to-Anterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
> file_code 1
> descrip FSL3.3
> aux_file
------------------------------------------------------------------------
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------
---
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