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: m...@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+ m...@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+ m...@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 m...@head1 ~/mcflirt_bug % mcflirt -in example4d.nii.gz -reffile ref.nii.gz -out example4d_mc m...@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 m...@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 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
