Hi Suzan, 

actually it uses rigid within-subject registration. 

The transformation files should be in ./mri/transforms (in long and in base). 

Best, Martin

On 17. Mar 2021, at 23:05, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Where is the non-linear registration coming from? Our long stream uses affine.

On 3/11/2021 2:59 PM, Suzan Maleki wrote:

Hi FS experts,

I appreciate it if you help me with a question on your longitudinal processing pipeline. If I use FreeSurfer to generate an unbiased T1 image template from N time points (non-linear registration), then how can I apply the within subject transformation matrix (Jacobian matrix) to that subject's DTI maps. 

Does FreeSurfer save the transformation matrix from N.Time-Points toward Template image? and if so, in which folder directory it will be saved? 

Also, given that FS uses vertices, should I first convert that transformation matrix to voxel space  (eg. using surf2voxels ?) and then multiply that into different time-points of one's DTI images.

Hope my questions are clear and looking forward to hearing from you:-)

Best 

Suzan 

--

Suzan Maleki

PhD Student

Brain, Mind and Society Research Hub

Turner Institute for Brain and Mental Health

School of Psychological Sciences

Monash University
770 Blackburn Road

Clayton VIC 3800 Australia

E: suzan.maleki@monash.edu
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