afni.nimh.nih.gov

Hi, Fabian-

So, just to be clear, you converted the dataset to show the brain in non-sphinx position (and hopefully left and right are still correct? That is the tricky one to verify...). Then you put this new dataset -- with a "standard" positioning, at least from a human brain perspective -- into @animal_warper and the warp was still weird? If that is the case, then a few things:

Could you please post your @animal_warper command that you are using? Having these details is useful (esp. to know what template you are using).

To know a bit more about this dataset, in particular if there is any obliquity could you please post the output of this command:

3dWarp   -deoblique   -disp_obl_xform_only  T1.nii.gz

There is a lot of outside-brain data in your scan; that might confuse the alignment. We can try adjusting for that (e.g., removing all the stuff way below the dataset). But first, I woud like to know what the relative alignment of your dataset at the start is to the template. Can you run this script, where you substitute the name of your "T1.nii.gz" where INPUT_DATASET is, and the name of your reference template where REFERENCE_DATASET is (and post the image it creates):

#!/bin/tcsh

set dset_src  =  INPUT_DATASET
set dset_ref  =   REFERENCE_DATASET

set opref_img = img_overlap

# ------------------------------------------------------------------------

set dset_cp_ref = __TMP_COPY_REF.nii.gz

# copy the ref and make sure the ref and src have the same space, to
# overlay for visualizing
3dcopy                                     \
    -overwrite                             \
    "${dset_ref}"                          \
    ${dset_cp_ref}

3drefit -space `3dinfo -space "${dset_src}"` "${dset_cp_ref}"

# ------- make image along each viewplane
@chauffeur_afni                        \
    -ulay  "${dset_src}"               \
    -olay  "${dset_cp_ref}"            \
    -pbar_posonly                      \
    -cbar Reds_and_Blues               \
    -set_subbricks 0 0 0               \
    -opacity 5                         \
    -prefix   "${opref_img}"           \
    -montx 1 -monty 1                  \
    -set_xhairs ON                     \
    -label_mode 1 -label_size 3        \
    -do_clean 

# glue separate images together
2dcat                                  \
    -gap 5                             \
    -gap_col 128 128 128               \
    -nx 3 -ny 1                        \
    -prefix "${opref_img}_FINAL.jpg"   \
    "${opref_img}".*.png

echo ""
echo "++ DONE.  Please check out this image for relative alignment/overlap:"
echo "     ${opref_img}_FINAL.jpg"
echo ""

# ... and you can delete the __TMP_COPY_REF.nii.gz file, if you want

exit 0

thanks,
pt