Dear AFNI gurus,

I encountered some strange behaviour when trying to apply @auto_tlrc to a functional dataset, that is with "Usage 2" that applies a transformation that was computed earlier. For some reason @auto_tlrc cannot

The commands I used are:

nick@head1:~/toy/mni/s02$ rm m01_fwhm0_raw_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+tlrc.*
nick@head1:~/toy/mni/s02$ @auto_tlrc -apar s02_SurfVol_ss_al2exp+tlrc -dxyz 3 -input m01_fwhm0_raw.nii.gz
Copying NIFTI volume to ./m01_fwhm0_raw_XYZ_OYmeqfZ3JqF7n9LNC7gDAA
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Jan 18 2013) [64-bit]
Error: Output dset m01_fwhm0_raw_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+tlrc exists

and it provides no output except the temporary HEAD and BRIK files that were removed in the first command.

For now I found a work around by first copying the NIFTI file to AFNI format, apply the transform, then copy the output to NIFTI. The full output is at the end of this message.

Still I am wondering why @auto_tlrc gets confused when using NIFTI files....

cheers,
Nick


========================
workaround
========================

nick@head1:~/toy/mni/s02$ 3dcopy m01_fwhm0_raw.nii.gz _a+orig
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Jan 18 2013) [64-bit]
nick@head1:~/toy/mni/s02$ @auto_tlrc -apar s02_SurfVol_ss_al2exp+tlrc -dxyz 3 -input _a+orig.
Applying tlrc warp from ./s02_SurfVol_ss_al2exp+tlrc to _a+orig ...
Padding the input data before warping
++ 3dZeropad: AFNI version=AFNI_2011_12_21_1014 (Jan 18 2013) [64-bit]
++ output dataset: ./__ats_tmp__ipad+orig.BRIK
Creating grid at (3 3 3)mm RAI resolution...
Warping per parent transform (quintic interpolation) and resampling with Bk interpolation (use -onewarp for single interpolation) ...
++ 3dWarp: AFNI version=AFNI_2011_12_21_1014 (Jan 18 2013) [64-bit]
++ Authored by: RW Cox
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Jan 18 2013) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__warp_grid+tlrc
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Jan 18 2013) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__a+orig
*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING: Consider changing the view of the dataset to TLRC view also
++ 3drefit processed 1 datasets
Changing view of xformed volumes
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Jan 18 2013) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__a+orig.HEAD
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_2011_12_21_1014 (Jan 18 2013) [64-bit]
++ Warning: ignoring +tlrc on new_prefix.
++ THD_rename_dataset_files: rename __ats_tmp__a+tlrc.HEAD -> _a+tlrc.HEAD
++ THD_rename_dataset_files: rename __ats_tmp__a+tlrc.BRIK -> _a+tlrc.BRIK
Cleanup ...
nick@head1:~/toy/mni/s02$ 3dcopy _a+tlrc _a_at.nii.gz
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Jan 18 2013) [64-bit]