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 #588147,
regarding fsl: mcflirt with referencefile doesn't put proper xform
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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--
588147: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=588147
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: fsl
Version: 4.1.5.2-3
Severity: normal
Hi,
when I mcflirt a timeseries and use a seperate reference volume as the
target mcflirt doesn't set the q/sform of the reference image as the
transformation setting in the output image. Instead is keeps the original
image transformation -- which is somewhat invalid after alignment.
Here is the demo:
mih@head1 ~/mcflirt_bug % fslinfo ref.nii.gz
data_type FLOAT32
dim1 64
dim2 64
dim3 48
dim4 1
datatype 16
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 3.0000000000
pixdim4 1.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
mih@head1 ~/mcflirt_bug % fslinfo example4d
data_type INT16
dim1 64
dim2 64
dim3 48
dim4 2
datatype 4
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 3.0000000000
pixdim4 3.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
mih@head1 ~/mcflirt_bug % nifti_tool -diff_hdr -infiles ref.nii.gz
example4d.nii.gz
name offset nvals values
------------------- ------ ----- ------
dim 40 8 3 64 64 48 1 1 1 1
dim 40 8 4 64 64 48 2 1 1 1
datatype 70 1 16
datatype 70 1 4
bitpix 72 1 32
bitpix 72 1 16
pixdim 76 8 -1.0 3.0 3.0 3.0 1.0 0.0 0.0 0.0
pixdim 76 8 -1.0 3.0 3.0 3.0 3.0 0.0 0.0 0.0
qoffset_x 268 1 66.162651
qoffset_x 268 1 70.5
qoffset_y 272 1 88.771057
qoffset_y 272 1 87.325317
qoffset_z 276 1 84.433723
qoffset_z 276 1 88.771057
srow_x 280 4 -0.0 -0.0 -3.0 66.162651
srow_x 280 4 -0.0 -0.0 -3.0 70.5
srow_y 296 4 -3.0 -0.0 -0.0 88.771057
srow_y 296 4 -3.0 -0.0 -0.0 87.325317
srow_z 312 4 0.0 -3.0 0.0 84.433723
srow_z 312 4 0.0 -3.0 0.0 88.771057
mih@head1 ~/mcflirt_bug % mcflirt -in example4d.nii.gz -reffile ref.nii.gz -out
example4d_mc
mih@head1 ~/mcflirt_bug % nifti_tool -diff_hdr -infiles example4d.nii.gz
example4d_mc.nii.gz
name offset nvals values
------------------- ------ ----- ------
cal_max 124 1 0.0
cal_max 124 1 1536.830566
mih@head1 ~/mcflirt_bug % nifti_tool -diff_hdr -infiles ref.nii.gz
example4d_mc.nii.gz
name offset nvals values
------------------- ------ ----- ------
dim 40 8 3 64 64 48 1 1 1 1
dim 40 8 4 64 64 48 2 1 1 1
datatype 70 1 16
datatype 70 1 4
bitpix 72 1 32
bitpix 72 1 16
pixdim 76 8 -1.0 3.0 3.0 3.0 1.0 0.0 0.0 0.0
pixdim 76 8 -1.0 3.0 3.0 3.0 3.0 0.0 0.0 0.0
cal_max 124 1 0.0
cal_max 124 1 1536.830566
qoffset_x 268 1 66.162651
qoffset_x 268 1 70.5
qoffset_y 272 1 88.771057
qoffset_y 272 1 87.325317
qoffset_z 276 1 84.433723
qoffset_z 276 1 88.771057
srow_x 280 4 -0.0 -0.0 -3.0 66.162651
srow_x 280 4 -0.0 -0.0 -3.0 70.5
srow_y 296 4 -3.0 -0.0 -0.0 88.771057
srow_y 296 4 -3.0 -0.0 -0.0 87.325317
srow_z 312 4 0.0 -3.0 0.0 84.433723
srow_z 312 4 0.0 -3.0 0.0 88.771057
--
GPG key: 1024D/3144BE0F Michael Hanke
http://mih.voxindeserto.de
--- 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 ---
