Hi,
I'm not sure if you'd had any reply to this, but I just wanted to note
that the cal_max and cal_min only control the display range. In FSLView
you can override these by specifying your own display range in the
boxes provided. So once you set your own range there should be no
difference between files with different cal_max/min if they contain the
same intensity information. However, if the intensities reported in the
voxels are not right, then it is something more serious.
Hope this helps.
All the best,
Mark
On 12 Apr 2009, at 02:26, Dianne Patterson wrote:
> Dear ImageJ and FSL groups,
> I realize now that the following information might also be helpful
> for solving the problem I submitted earlier.
>
> All of these mask images are on a single slice, other slices in the
> volume have been set to 0 using fslmaths.
>
> In the "good" images (the masks that correctly display in fslview
> the lines I drew in ImageJ), the following values appear: 32767
> corresponds to my original corpus callosum mask.
> -32768 corresponds to the black background
> 0 corresponds to the lines I drew in ImageJ and to the uninteresting
> slices
> (in these, cal_max=1 and cal_min=0)
>
> In the "bad" images: 32767 corresponds to the original corpus
> callosum mask.
> -32768 corresponds to the black background
> 0 correspond to the uninteresting slices that I'd set to zero
> previously.
> However, the lines made in imageJ do not appear (and mousing around
> suggests that the values are not there at all.
> (in these
> cal_max 32768.0000
> cal_min -32768.0000)
>
> I have appended my original message below with 2 sample headers
> generated by fslhd.
>
> Thanks,
>
> Dianne
> --
> Dianne Patterson, Ph.D.
> [log in to unmask]
> University of Arizona
> SLHS 328
> 621-5105
>
>
> Dear Group,
> I do some editing in ImageJ, creating lines and angles, then save
> those back into Nifti-1 format.
> For most images processed in FSL 4.X after May 2008, I can view the
> lines and angles in fslview.
>
> When I looked at the headers for the older images, I saw that they
> lacked intent codes, so I added those.
>
> intent_code = '1002'
> intent_p1 = '0'
> intent_p2 = '0'
> intent_p3 = '0'
> About half of the older images display the lines and angles just
> fine since I added the intent codes to the headers.
>
> However, something more subtle (to me anyhow) still seems to be
> causing trouble in about 1/2 of the older images and 1 of the newer
> images.
>
> It seems that cal_max and cal_min look like this in the misbehaving
> files:
> cal_max 32768.0000
> cal_min -32768.0000
> ----------
> but cal_max and cal_min look like this in the well-behaved files
> cal_max 1.0000
> cal_min 0.0000
> are just fine.
>
> It seems that ImageJ is changing the values from 1 and 0 (which they
> are before I import them) to 32768 and -32768...
> but I presume something else in the header must be causing ImageJ to
> treat this handful of image differently.
>
> I am including a good header and a bad header in case I'm missing
> something, and I'm sending this to both FSL and ImageJ listserves...
> since the problem seems to fall in between somewhere. Any insights
> would be greatly appreciated.
>
> Thankyou for your time.
> =========================
> A newer file that is misbehaving (after ImageJ Processing)
> =========================
> filename CC/cc-dpJ.nii
>
> sizeof_hdr 348
> data_type INT16
> dim0 4
> dim1 128
> dim2 57
> dim3 128
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units Unknown
> time_units Unknown
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 1.0000000000
> pixdim2 1.0000000000
> pixdim3 1.0000000000
> pixdim4 1.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 352
> cal_max 32768.0000
> cal_min -32768.0000
> 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 Label index
> intent_code 1002
> intent_name
> intent_p1 0.000000
> intent_p2 0.000000
> intent_p3 0.000000
> qform_name Scanner Anat
> qform_code 1
> qto_xyz:1 0.000000 0.000000 -1.000000 166.955002
> qto_xyz:2 1.000000 0.000000 -0.000000 -142.800690
> qto_xyz:3 0.000000 1.000000 -0.000000 -64.605103
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Posterior-to-Anterior
> qform_yorient Inferior-to-Superior
> qform_zorient Right-to-Left
> sform_name Scanner Anat
> sform_code 1
> sto_xyz:1 0.000000 0.000000 -2.601560 166.955002
> sto_xyz:2 2.601560 0.000000 0.000000 -142.800690
> sto_xyz:3 0.000000 2.600002 0.000000 -64.605103
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Posterior-to-Anterior
> sform_yorient Inferior-to-Superior
> sform_zorient Right-to-Left
> file_type NIFTI-1+
> file_code 1
> descrip FSL4.0
> aux_file
> =====================
> A newer file that is behaving correctly (header after ImageJ
> Processing)
> =====================
> filename CC/cc-dpJ.nii
>
> sizeof_hdr 348
> data_type INT16
> dim0 4
> dim1 128
> dim2 57
> dim3 128
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units Unknown
> time_units Unknown
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 1.0000000000
> pixdim2 1.0000000000
> pixdim3 1.0000000000
> pixdim4 1.0000000000
> pixdim5 1.0000000000
> pixdim6 1.0000000000
> pixdim7 1.0000000000
> vox_offset 352
> cal_max 1.0000
> 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 Label index
> intent_code 1002
> intent_name
> intent_p1 0.000000
> intent_p2 0.000000
> intent_p3 0.000000
> qform_name Scanner Anat
> qform_code 1
> qto_xyz:1 0.000000 0.000000 -1.000000 170.466995
> qto_xyz:2 1.000000 0.000000 -0.000000 -142.800995
> qto_xyz:3 0.000000 1.000000 -0.000000 -51.141701
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Posterior-to-Anterior
> qform_yorient Inferior-to-Superior
> qform_zorient Right-to-Left
> sform_name Scanner Anat
> sform_code 1
> sto_xyz:1 0.000000 0.000000 -2.601560 170.466995
> sto_xyz:2 2.601560 0.000000 0.000000 -142.800995
> sto_xyz:3 0.000000 2.600000 0.000000 -51.141701
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Posterior-to-Anterior
> sform_yorient Inferior-to-Superior
> sform_zorient Right-to-Left
> file_type NIFTI-1+
> file_code 1
> descrip FSL4.0
> aux_file
> --
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