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 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". 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