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, cabe@uos.de wrote:

thanks, that was already helpful.

But does the fact that the transformation is carried out affect the results? I mean, the images has to be resliced and interpolated during this transformation. So intensities change slightly. If i would process the same subject, once with and once without an reorientation in the beginning as start input data, would you expect a difference?

Or in other words, if you would compare groups, where one group was AC-PC aligned with SPM before freesurfer processing and the other was not, could any of the differences be attributed to the different input files (transformation matrix in the nii header).

Chris

...

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, cabe@uos.de wrote:

...

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 tkmedit, the images are tilted (AC-PC aligned). So it seems that freesurfer reads and applies the transformation saved in the nii file.

Is that true? and if yes at which step?

When using the recon-all -i command to create the starting folders and mgz files before starting the actual freesurfer processing, is the transformation matrix used to realign the images during this first process, and the following processing is done on the reoriented image? or is it just used for display? Or is the fact that the image appears tilted a result of the Talairach transform and the nii header was not read at all?

I am asking because, I have subjects which were SPM aligned, and subject which were not. I am wondering if it makes any difference, since due to an initial reorientation data will be interpolated and maybe a bit smoothed, compared to data which was not aligned before.

Does anybody have any experience with that and a feeling if an reorientation beforehand would have an effect on the outcome for cortical thickness maesures?

Thaks for any comments, Chris

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