Hi Paul, chiming in here (Irene and I are form the same lab and we are using the script we ended up with after my last thread). If I remember correctly we talked about how to handle obliquity. I used one of your options from here, i.e. purging the obliquity information.

Firstly I attach a print of the tempalte with test_copy.nii as the overlay generated by:

3dcopy  ${T1_data} test_copy.nii
3drefit -space TLRC test_copy.nii

We can see that the top of the brain is outside the FOV.

Secondly this is the output of 3dWarp -disp_obl_xform_only -deoblique ${T1_data} pointing at the raw data (the data is from the same imaging center).

# mat44 Obliquity Transformation ::
      0.999133      0.012294     -0.039781      -4.534111
     -0.023566      0.954632     -0.296853     -14.104416
      0.034327      0.297533      0.954094     -46.005127

The typical output for me when running the same script as Irene is that the datasets below are clipped (seem to be same are as my first attachment):
anatSS
anatSS_al_junk
anatSS_flip_al_junk
anatSS_unflipped
anatSS_unflipped_ob
anatSS_unflipped_ob_temp_al_junk

While these look fine (including anat_final)
anatQQ
anatSS_unflipped_ob_al_junk_wtal
anat_final
follow_anat_anat_w_skull
anatQQ_WARP.nii
stats

Attaching anat _final and anatSS side by side (all of the top dsets look like the anatSS).


I think Irene hade the clipping in the anat_final as well. But how come all those top dsets beeing clipped does not affect the anat_final (in my case)?

But we can try your first suggestion:

@Align_Centers \
   -cm \
   -prefix NEW_anat -dset subj.anat.uni+orig. \
  -base ~/abin/TT_N27_SSW.nii.gz

Where we use our raw t1.nii data and the MNI157_2009_SSW.nii tempalte (right?).

EDIT: The pre-center solved the clipping in my dataset. But I still wonder why anat_final was OK before even though all of these:
anatSS
anatSS_al_junk
anatSS_flip_al_junk
anatSS_unflipped
anatSS_unflipped_ob
anatSS_unflipped_ob_temp_al_junk
Where clipped



Edited 2 time(s). Last edit at 04/28/2020 07:27AM by Robin.