Hi,

I am trying to align the data on an imagination experiment of Tabelow and Polzehl (Journal of Statistical Software, 2011) paper available at:

[www.jstatsoft.org]

(The above link contains the dataset.)

The authors in private e-mail have confirmed that the dataset are not registered -- either for motion correction in the functional time course sequence of image volumes or to the anatomical. So, I have been trying to use align_epi_anat.py for this purpose before doing my analyis in R/C.

The functional dataset has the following characteristics:

NIfTI-1 format
Type : nifti
Data Type : 4 (INT16)
Bits per Pixel : 16
Slice Code : 0 (Unknown)
Intent Code : 0 (None)
Qform Code : 0 (Unknown)
Sform Code : 1 (Scanner_Anat)
Dimension : 64 x 64 x 30 x 105
Pixel Dimension : 3.75 x 3.75 x 4 x 2
Voxel Units : mm
Time Units : sec

The anatomic dataset has the following:
target
NIfTI-1 format
Type : nifti
Data Type : 4 (INT16)
Bits per Pixel : 16
Slice Code : 0 (Unknown)
Intent Code : 0 (None)
Qform Code : 0 (Unknown)
Sform Code : 1 (Scanner_Anat)
Dimension : 110 x 208 x 202
Pixel Dimension : 1.5 x 0.94 x 0.94
Voxel Units : mm
Time Units : sec

Anyway, so I want to align the functional data on to the anatomic and then get a common grid so that I can overlay the functional on top of the anatomic (after doing some computations on the functional images).

The anatomic image is 110 x 208 x 202 while the functional is 64 x 64 x 30 x 105. So, I tried the following:

align_epi_anat.py -anat MPRAGEco.nii.gz -epi Imagination.nii.gz  -epi_base 6 -save_vr

but the new datasets still have the same old dimension. The question is: how do I get them to match each other so that I can plot one on top of the other using R. (I know the latter part, but getting the grid right is what I am asking about).

I apologize but all this is very new to me. I also tried Talaraiching using the following:

@auto_tlrc -base ~/abin/TT_N27+tlrc -input MPRAGEco.nii.gz 
align_epi_anat.py -anat MPRAGEco.nii.gz -epi Imagination.nii.gz -epi_base 6 -epi2anat -tlrc_apar MPRAGEco_at.nii

but what came out were new anatomical and functional images which did not match each other's dimensions in the image volume.

Apologies again if these questions are trivial and based on an incorrect understanding of AFNI's working.

Many thanks again for your time in reading and thinking about my question and the answer!!

Best wishes,
Ranjan