On Fri, May 1, 2009 at 4:41 AM, Mark Jenkinson
<[log in to unmask]> wrote:
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
--
