hello all,

Registration of a volume and functionals into tlrc space has been a problem for me for quite some time now. I have bugged this board by asking a lot of silly questions before and so am continuing to do so as I am now totally confused. I do not know much about anatomy and so am trying to avoid using AFNI tools of marking the AC-PC etc (as I might mark them wrong), aligning to AC-PC and then getting the data into Talaraich space. I have tried using FSL-FLIRT algorithm and mritotal and mincresample in MINC.

I have the following concerns:
1. In case of FSL, I used their standard template which is the avg152 brain. I used 3dAFNItoANALYZE, then FSL-FLIRT and then 3dcopy to get the nii file back to AFNI. I understand that even though I have got an "orig" format dataset now it is registered to the avg152template. As I want to avoid using the AC-PC etc, thought I could use 3drefit -view tlrc to observe it in tlrc which I could. But I guess this isnt the correct way to do it cause the voxel size, extent, number of voxels etc is different. So for e.g. if I launch the TTatlas the areas would be all haywire.
Could anyone please suggest a proper method of doing this in FSL and getting it back into AFNI.

2. I also did try MINC. The MINC brain is bigger and so even though I have a tlrc brain after using 3dAFNItoANALYZE, mritotal, mincresample, 3dcopy , I get a larger brain datset. Back again, though it is in tlrc space, being a bigger brain, dont think ttatlas etc would work. Could anyone suggest a method of how to go about doing this in MINC.

3. I have received feed back from people who suggested that with functional data, I could just adwarp onto a given template or also adwarp onto the volume which has been registered to a template already. Could I just do adwarping or should I be registering the functional data to these templates? I tried registering the time series and then ran 3dDeconvolve and also tried running 3dDeconvolve first and then registering. The picture looks nice but with the dimensions being all haywire I dont think it is correct.

4. Is there any other software I should play aaround with or just stop doing so as I am already confused.

Please do help.

thanks
nameeta