Hi Knut

the flip angle in the header shouldn't change anything, although you can use mri_copy_params from a volume with the correct parameters.

As for your second question, that's tougher. Why were they changed? Are you sure they are correct? Was the data resampled?

cheers Bruce

On Sat, 7 Jan 2012, Knut J Bjuland wrote:

Hi I have problem with two dataset processed with different version of Freesurfer but with the same subject. I am able to import the data set proceed with Freesurfer 4.30 into Freesurfer 5.1. But there was used some proprietary programs at FS 430 data for motion correction and contrast enhancement before the dicom files was input into Freesurfer. These proprietary programs change the flip angle from 7 degrees to 401.07 degrees. I am able to replicate findings that survive FDR but I get quite different result for findings that do not survive FDR. My theory is that the proprietary programs change the dicom in such manner that it gives a new dicom files. Is this correct? I do not have access to these programs anymore. What effect will it give if software is used to change flip angle on a dicom image? Can I use Freesurfer to force the flip angle back to 7 degree? I converted the files from Freesurfer 4.30 to Freesurfer 5.1 using recon ?make all ?s {subject}. I am enclosing the mri_info of the first files in Freesurfer pipeline.

The vox to ras and ras to voxel is also changed. What effect will this have?

Knut J