Dear AFNI experts,

We recently acquired EPI and anatomical scans on two different sessions:


First session: EPI_1
EPI_2
Anatomical_1
EPI_3
EPI_4

Second session: Anatomical_2
EPI_5


I would like to register the EPI_5 scan and the anatomical_2 scan from the second session to the anatomical scan and EPI data from the first session, to combine the data. However, I am unsure as to the best way to proceed.

Should I use something like this:

3dvolreg -twopass -twodup -heptic -clipit -base Anatomical_1+orig \
-prefix Anatomical_2_al Anatomical_2+orig

3drotate -heptic -clipit -rotparent Anatomical_2_al+orig -gridparent EPI_1+orig \
-prefix EPI_5_al EPI_5+orig


Once the second session is aligned to the first session, can I align using 3dvolreg all the EPIs (5 total) to one EPI reference scan from the first session (in this case EPI_2).

For EPI_1:
3dvolreg -twopass -tshift 20 -dfile EPI_1.Motion -prefix EPI_1.mc+orig -base EPI_2+orig'[10]' EPI_1+orig

For EPI_2:
3dvolreg -twopass -tshift 20 -dfile EPI_2.Motion -prefix EPI_2.mc+orig -base EPI_2+orig'[10]' EPI_2+orig

For EPI_3:
3dvolreg -twopass -tshift 20 -dfile EPI_3.Motion -prefix EPI_3.mc+orig -base EPI_2+orig'[10]' EPI_3+orig

For EPI_4
3dvolreg -twopass -tshift 20 -dfile EPI_4.Motion -prefix EPI_4.mc+orig -base EPI_2+orig'[10]' EPI_4+orig

For EPI_5

3dvolreg -twopass -tshift 20 -dfile EPI_5.Motion -prefix EPI_5.mc+orig -base EPI_2+orig'[10]' EPI_5_al+orig


and then align the two anatomical scans to this reference scan:

align_epi_anat.py -volreg off -tshift off -anat2epi -epi EPI_2+orig -anat Anatomical_2_al+orig -epi_base 10

align_epi_anat.py -volreg off -tshift off -anat2epi -epi EPI_2+orig -anat Anatomical_1+orig -epi_base 10


Thank you in advance for your help,

Isabelle