Hi Nick,
Yes, 10017.GM.nii' is in '/home/AD/ebelleau/Desktop/nas/MRI/RumMR/FreeSurfer/10017/SUMA'.
Here is the full output:
[ebelleau@psy-imglab-7 RumMR_Scripts_ICA]$ ./Warp_Freesurfer_MNI_final
Copying NIFTI volume to ./10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Mar 22 2013) [64-bit]
*+ WARNING: Disk space: writing file ./10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK (16 MB), but only 0 free MB on disk
Performing center alignment with @Align_Centers
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Mar 22 2013) [64-bit]
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Mar 22 2013) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_2011_12_21_1014 (Mar 22 2013) [64-bit]
++ THD_rename_dataset_files: rename 10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD -> __ats_tmp__10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD
++ THD_rename_dataset_files: rename 10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK -> __ats_tmp__10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK
** THD_rename_dataset_files: old header 10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+acpc.HEAD doesn't exist!
** THD_rename_dataset_files: old header 10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA_shft+tlrc.HEAD doesn't exist!
++ 3dWarp: AFNI version=AFNI_2011_12_21_1014 (Mar 22 2013) [64-bit]
++ Authored by: RW Cox
*+ WARNING: Disk space: writing file ./pre.10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK (16 MB), but only 0 free MB on disk
Error: Anatomical dset pre../10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEAD not found.
Thanks so much for all of your help!
Emily