Your message dated Fri, 24 Jun 2022 14:48:37 +0000
with message-id <[email protected]>
and subject line Bug#1009276: Removed package(s) from unstable
has caused the Debian Bug report #616006,
regarding diverging sform from qfrom after basic linear flirting (could be
related to #588147)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
616006: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=616006
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: fsl-4.1
Version: 4.1.7-1
Severity: normal
File: /usr/lib/fsl/4.1/flirt
Tags: upstream
After reslicing harvard oxford cortical atlas (having identical q- and s-
forms:
qform_code 2
qto_xyz:1 -2.000000 0.000000 -0.000000 90.000000
qto_xyz:2 0.000000 2.000000 -0.000000 -126.000000
qto_xyz:3 0.000000 0.000000 2.000000 -72.000000
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 Aligned Anat
sform_code 2
sto_xyz:1 -2.000000 0.000000 0.000000 90.000000
sto_xyz:2 0.000000 2.000000 0.000000 -126.000000
sto_xyz:3 0.000000 0.000000 2.000000 -72.000000
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
into the subject space using flirt:
flirt -in
/usr/share/fsl/data/atlases/HarvardOxford/HarvardOxford-cort-prob-2mm.nii.gz
-ref bold_mean.nii.gz -init trans/mni2bold.mat -applyxfm -out
HarvardOxford-cort-prob-bold-2.nii.gz
qform and sform carry different values:
$> fslhd HarvardOxford-cort-prob-bold-2.nii.gz | grep -A 100 form_code
qform_code 2
qto_xyz:1 -3.495180 -0.123161 -0.153425 86.463974
qto_xyz:2 -0.143651 3.655497 0.822284 -164.003738
qto_xyz:3 -0.114382 -0.827449 3.655518 -96.569008
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 Aligned Anat
sform_code 2
sto_xyz:1 -3.973516 -0.117754 -0.152804 86.463974
sto_xyz:2 -0.181955 4.048423 0.851950 -164.003738
sto_xyz:3 -0.142902 -0.994334 4.139136 -96.569008
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
which in turn confuses nibabel, which takes the sform as the ultimate
affine transformation and computes voxel sizes to be 3.98024607, 4.1704073 ,
4.22866583 instead of the original 3.5, 3.75, 3.75 in the target space given by
bold_mean.nii.gz.
The header of bold_mean.nii.gz :
$> fslhd bold_mean.nii.gz
filename bold_mean.nii.gz
sizeof_hdr 348
data_type INT16
dim0 3
dim1 40
dim2 64
dim3 64
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 3.5000000000
pixdim2 3.7500000000
pixdim3 3.7500000000
pixdim4 2.5000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 352
cal_max 2668.0000
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 Unknown
qform_code 0
qto_xyz:1 3.500000 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 3.750000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 3.750000 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 FSL4.0
aux_file
-- System Information:
Debian Release: wheezy/sid
APT prefers testing
APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100,
'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.37-1-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Versions of packages fsl-4.1 depends on:
ii bc 1.06.95-2 The GNU bc arbitrary precision cal
ii chromium-browser [ww 9.0.597.98~r74359-1 Chromium browser
ii csh [c-shell] 20070713-2 Shell with C-like syntax, standard
ii dc 1.06.95-2 The GNU dc arbitrary precision rev
ii fslview 3.1.8+4.1.6-2 viewer for (f)MRI and DTI data
ii iceweasel [www-brows 3.6.13-2 Web browser based on Firefox
ii konqueror [www-brows 4:4.4.5-2 advanced file manager, web browser
ii libc6 2.11.2-11 Embedded GNU C Library: Shared lib
ii libgcc1 1:4.4.5-12 GCC support library
ii libgd2-xpm 2.0.36~rc1~dfsg-5 GD Graphics Library version 2
ii libgdchart-gd2-noxpm 0.11.5-7 Generate graphs using the GD libra
ii libnewmat10ldbl 1.10.4-5 matrix manipulations library (C++)
ii libnifti2 2.0.0-1 IO libraries for the NIfTI-1 data
ii libpng12-0 1.2.44-1 PNG library - runtime
ii libstdc++6 4.4.5-12 The GNU Standard C++ Library v3
ii links [www-browser] 2.3~pre1-1 Web browser running in text mode
ii lynx-cur [www-browse 2.8.8dev.8-1 Text-mode WWW Browser with NLS sup
ii opera [www-browser] 9.64.2480.gcc4.qt3 The Opera Web Browser
ii tcl8.4 8.4.19-4 Tcl (the Tool Command Language) v8
ii tcsh [c-shell] 6.17.02-4 TENEX C Shell, an enhanced version
ii tk8.4 8.4.19-4 Tk toolkit for Tcl and X11, v8.4 -
ii w3m [www-browser] 0.5.3-1 WWW browsable pager with excellent
ii zlib1g 1:1.2.5.dfsg-1 compression library - runtime
Versions of packages fsl-4.1 recommends:
ii fsl-atlases 4.1.6-3 FSL's MNI152 standard space stereo
ii fsl-doc-4.1 4.1.7-1 documentation for FSL
Versions of packages fsl-4.1 suggests:
ii dicomnifti 2.28.15-1 converts DICOM files into the NIfT
pn fsl-feeds <none> (no description available)
pn fsl-first-data <none> (no description available)
pn fsl-possum-data <none> (no description available)
pn gridengine-client <none> (no description available)
ii octave3.2 3.2.4-8 GNU Octave language for numerical
-- no debconf information
--- End Message ---
--- Begin Message ---
Version: 5.0.8-6+rm
Dear submitter,
as the package fsl has just been removed from the Debian archive
unstable we hereby close the associated bug reports. We are sorry
that we couldn't deal with your issue properly.
For details on the removal, please see https://bugs.debian.org/1009276
The version of this package that was in Debian prior to this removal
can still be found using http://snapshot.debian.org/.
Please note that the changes have been done on the master archive and
will not propagate to any mirrors until the next dinstall run at the
earliest.
This message was generated automatically; if you believe that there is
a problem with it please contact the archive administrators by mailing
[email protected].
Debian distribution maintenance software
pp.
Thorsten Alteholz (the ftpmaster behind the curtain)
--- End Message ---
