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
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 ftpmaster@ftp-master.debian.org. Debian distribution maintenance software pp. Thorsten Alteholz (the ftpmaster behind the curtain)