Re: [Freesurfer] Is transformation matrix in .nii (nifti) header applied by FS?

2013-11-14 Thread Douglas N Greve
you will see some differences due to reslicing and interpolation. These differences should be somewhat random, so they might be difficult to detect in a group analysis. But in general, you should treat all your data the same. On 11/14/2013 03:40 PM, c...@uos.de wrote: > thanks, that was alre

Re: [Freesurfer] Is transformation matrix in .nii (nifti) header applied by FS?

2013-11-14 Thread Douglas N Greve
There are two matrices in the nifti file (qform and sform). By default we use the qform. The qform is 6 dof and so is probably not appropriate for your talairach transform. Bottom line is that the sform is probably being ignored. doug On 11/14/2013 07:18 AM, c...@uos.de wrote: > Hello, > > I

[Freesurfer] Is transformation matrix in .nii (nifti) header applied by FS?

2013-11-14 Thread cabe
Hello, I have a question regarding nifti (.nii) input files. I have .nii image files, which are aligned to AC-PC with SPM. The actual (original) data in this file is not changed, but the transformation matrix is saved in the .nii file. When displaying the freesurfer reconstructed results with tkm