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Hello András,

Thanks so much for your help. I've tried the epi_reg flag, but it told me that "epi_reg command not found". I tried other flags such as flirt, it worked well. So I couldn't figure out what's the problem.

I read the information on flswiki_fat userguide page (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Label_files), and found that, I should "first transform the labels into a surface file, using the label2surf command", but the label2surf can't be found either. Have you ever encountered similar problems? And I wondered that, if it was reason that I couldn't register my roi (V1, obtained by converting freesurfer label file to a roi.nii using mri_label2vol flag).

Thanks again for your kind help!

Best wishes
Yours lulu
 


2013/5/19 Dr. András Jakab <[log in to unmask]>
Hello,

This is not the optimal way, I guess. Affine tfm should be enough and by using FLIRT's epi_reg you should be able to register the B0 to the FAST segmented T1 structural image quite precisely:


Otherwise if you really need nonlinear deformation, register the FA and T1 separately to the FMRIB58 and MNI152 templates, and from that space, you can transform ROIs back to either diffusion or native space. Transformation matrices and fields can be inverted as well.

Hope this helps.
Regards,
András

Dr. Andras Jakab, MD, PhD
Post Doctoral Researcher / University Assistant Lecturer
Department of BioMedical Laboratory and Imaging Science
Faculty of Medicine, University of Debrecen
98. Nagyerdei Krt.
4032 Debrecen
Hungary
Phone: +3652255170
Cellular: +36305095083


On Fri, May 17, 2013 at 4:36 PM, lujiao luo <[log in to unmask]> wrote:
Hello experts,

I was trying to warp a native space roi file into diffusion space (register with nodif_brain). I've tried several ways, but I couldn't obtain fine results. Is their someone would like to share this experience with me.
The command I used:

flirt -in t1.nii.gz -ref nodif_brain.nii.gz -out t1_to_nodif_trilinear.nii.gz -omat t1_to_nodif.mat -bins 256 -cost corratio -dof 12

 

fnirt --ref=nodif_brain --in=t1.nii.gz --refmask=nodif_brain_mask.nii.gz --iout=t1_to_nodif_fnirt.nii.gz --aff=t1_to_nodif_trilinear.mat –cout=t1_to_nodif_fnirt_cout

and then apply matrix file  t1_to_nodif.mat to my roi file which was segmented from the T1.nii.gz file.


I would be grateful for any help.