Dear all,
For a connectivity analysis I produce 2 upper-triangular matrices that I put together in a 2-slice NIfTI file. The planes are quite big (7666x7666 points) but that should not give memory problems on my system. I have set all irrelevant dimensions etc to 1:
fslinfo c1s003a1001_noneck_gmnet.nii.gz
data_type FLOAT32
dim1 7666
dim2 7666
dim3 2
dim4 1
datatype 16
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.000000
pixdim4 1.000000
cal_max 1.0000
cal_min -1.0000
file_type NIFTI-1+
At closer inspection, I cannot find anything wrong with the data either:
fslhd c1s003a1001_noneck_gmnet.nii.gz
filename c1s003a1001_noneck_gmnet.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 7666
dim2 7666
dim3 2
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.000000
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.000000
pixdim4 1.000000
pixdim5 1.000000
pixdim6 1.000000
pixdim7 1.000000
vox_offset 352
cal_max 1.0000
cal_min -1.0000
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 Unknown
qform_code 0
qto_xyz:1 1.000000 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 1.000000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 1.000000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
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 1
descrip grey matter shape correspondence
aux_file
and in matlab I can open the file with Jimmy Shen's NIfTI toolbox and plot the 2 planes with imshow().
When I open the file in FSLeyes though, I get these error messages on the command line a couple of times:
(fsleyes:9428): Gtk-WARNING **: 11:29:48.755: Negative content width -17 (allocation 1, extents 9x9) while allocating gadget (node button, owner GtkToggleButton)
(fsleyes:9428): Gtk-WARNING **: 11:29:48.755: Negative content height -9 (allocation 1, extents 5x5) while allocating gadget (node button, owner GtkToggleButton)
(fsleyes:9428): Gtk-WARNING **: 11:29:48.758: Negative content width -17 (allocation 1, extents 9x9) while allocating gadget (node button, owner GtkButton)
(fsleyes:9428): Gtk-WARNING **: 11:29:48.758: Negative content height -9 (allocation 1, extents 5x5) while allocating gadget (node button, owner GtkButton)
(64 lines in total)
In the FSLeyes window an error message appears saying:
An error occurred updating the texture data
Details: GLError(
err = 1281,
description = 'invalid value',
baseOperation = glTexImage3D,
pyArgs = (
GL_TEXTURE_3D,
0,
GL_R32F,
7666,
7666,
2,
0,
GL_RED,
GL_FLOAT,
None,
),
cArgs = (
GL_TEXTURE_3D,
0,
GL_R32F,
7666,
7666,
2,
0,
GL_RED,
GL_FLOAT,
None,
)
cArguments = (
GL_TEXTURE_3D,
0,
GL_R32F,
7666,
7666,
2,
0,
GL_RED,
GL_FLOAT,
None,
)
)
This means absolutely nothing to me. Is there a Python / OpenGL expert who can solve this?
The only dodgy thing syntactically is the comma followed by a bracket, but that can hardly be caused by the input image...
Thanks for your help!
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