Hi there,

In one of my subjects auto_warp.py failed to do the affine step by itself. Therefore I tried to calculate before the affine transform with 3dAllineate:
3dAllineate -base ${TEMPLATEDIR}/${TEMPLATE}'[0]' -input ${SUBJ}_T1_ns_bc.nii.gz -1Dmatrix_save extra.1D -prefix prueba.nii.gz

I checked and the images are aligned successfully. I tried to give the extra.1D matrix to auto_warp.py to skip the automatic affine step:

auto_warp.py -overwrite -base ${TEMPLATEDIR}/${TEMPLATE}'[0]' -input prueba.nii.gz -skull_strip_input no -affine_input_xmat 'extra.1D'

However, it gave me this error:
#++ auto_warp.py version: 0.04
# Output directory /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/
#Script is running:
mkdir /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/
mkdir: cannot create directory `/bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/': File exists
cd /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/
#Script is running:
rm /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/anat.nii
#Script is running (command trimmed):
3dcopy /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/prueba.nii.gz ./anat.nii
++ 3dcopy: AFNI version=AFNI_18.2.06 (Jul 31 2018) [64-bit]
#Script is running:
rm /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/anat.un.nii
#Script is running (command trimmed):
3dUnifize -GM -input ./anat.nii -prefix ./anat.un.nii
++ 3dUnifize: AFNI version=AFNI_18.2.06 (Jul 31 2018) [64-bit]
+ Pre-processing: ADV........UWG
++ Output dataset ./anat.un.nii
++ ===== Elapsed = 7.9 sec
#Script is running:
rm /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/base.nii
#Script is running (command trimmed):
3dcopy /export/home/vferrer/public/PARK_VFERRER/TEMPLATES_ATLAS/MNI152_2009_template_FSL.nii.gz ./base.nii
++ 3dcopy: AFNI version=AFNI_18.2.06 (Jul 31 2018) [64-bit]
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /export/home/vferrer/public/PARK_VFERRER/TEMPLATES_ATLAS/MNI152_2009_template_FSL.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
#++ Aligning /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/base.nii data to /bcbl/home/public/PARK_VFERRER/PREPROC/sub-029ParkEglPb/anat/awpy/anat.un.nii data
#Script is running (command trimmed):
3dWarp -matvec_out2in extra.1D -prefix ./anat.un.aff.nii ./anat.un.nii
++ 3dWarp: AFNI version=AFNI_18.2.06 (Jul 31 2018) [64-bit]
++ Authored by: RW Cox
** FATAL ERROR: Can't read -matvec file extra.1D
** Program compile date = Jul 31 2018
#**ERROR Failed in affine step
** ERROR - script failed
I have checked and the extra.1D file looks like this with cat_vect:
0.960819 0.0413537 -0.101087 -1.88474
0.0722554 0.78104 0.443372 -19.1824
0.0627243 -0.520414 0.699751 -16.6196

and like this with cat:
# 3dAllineate matrices (DICOM-to-DICOM, row-by-row):
0.960819 0.0413537 -0.101087 -1.88474 0.0722554 0.78104 0.443372 -19.1824 0.0627243 -0.520414 0.699751 -16.6196
Could you tell me what have i been doing wrong?

Cheers,
Vicente