Dear toolbox developers,

I just started using your toolbox, and I have a question here.

The output of your matlab routine "RFREG_pmap" and "RFREG_out" are in the space of the T1-weighted image. How do I transform it back to the FLAIR image space? I wanted to compare the results with the manual segmentation, which is done on the native FLAIR image.

I appreciate your help!!

Regards,

Dan Wu

Hello.

If you have access of T1 for your manually segmented images, then you can compute the transformation between T1 and FLAIR and apply it to the manually segmented binary (or other) image. This should be done individually for each subject.
Or another option is to compute the average T1 and FLAIR images for your data -- and use this one transformation map for all images.
Keep in mind that any warping of the spaces "after" segmentation is done is going to induce some errors on detection boundaries.

I would suggest comparing things in T1 space instead of FLAIR mainly because FLAIR is more sensitive to registration/warping errors than T1. See Spm8/Spm12 manual for further suggestions.

Hi Vamsi,

Thank you for the reply! 

Yes, I need a transformation matrix to transform my manually segmented WMH maps (in the FLAIR image space) to T1. Does your matlab routine produce such matrix when it does the FLAIR-to-T1 registration?

Thanks,

Dan

The preprocessing is handled by WhyD_preproc.m
Although main processing files are stored, this particular transformation map is not. Spm8 however allows one to store them. You can change the storing variables in the above script file, or better, simply run spm8 warp routine on T1 and FLAIR native spaces and get the transformations. After that you can apply them one at a time to your manual segmentations. This is easier. See spm8 warp and normalize modules.