I appear to get an error converting anatomical data to MNI space. My old command used to use MNI152_T1_2009c+tlrc from a shared folder and this worked. The old working code was:

@auto_tlrc -base /usr/share/afni/atlases//MNI152_T1_2009c+tlrc. -input $sid.anat+orig.

However, in order to run my script through multiple servers and not risk two servers trying to access the same template file at the same time, I decided to copy the shared MNI152 template into my own folder with different names per subject using these lines:

cp /usr/share/afni/atlases/MNI152_T1_2009c+tlrc.HEAD $HomePath/MNI152_T1_2009c_$sid+tlrc.HEAD
cp /usr/share/afni/atlases/MNI152_T1_2009c+tlrc.BRIK.gz $HomePath/MNI152_T1_2009c_$sid+tlrc.BRIK.gz

Then, I changed my @auto_tlrc command as follows:

@auto_tlrc -base $Templates/MNI152_T1_2009c_$sid+tlrc. -input $sid.anat+orig.

However, this no longer creates a tlrc version of my anatomy file. Instead I get the following error:

*********** Warning *************
Dataset centers are 54.027475 mm
apart. If registration fails, or if
parts of the original anatomy gets
cropped, try adding option
-init_xform AUTO_CENTER
to your @auto_tlrc command.

*********************************

Padding ...
++ 3dZeropad: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ output dataset: ./__ats_tmp__ref_MNI152_T1_2009c_CI_001_M4_40pad+tlrc.BRIK
Skull Stripping ...
Warning 3dSkullStrip:****************
Surface self intersecting! trying again:
smoothing of 84, avoid_vent -1
Warning 3dSkullStrip:****************
Surface self intersecting! trying again:
smoothing of 96, avoid_vent -1
Warning 3dSkullStrip:****************
Surface self intersecting! trying again:
smoothing of 108, avoid_vent -1
Warning 3dSkullStrip:****************
Surface self intersecting! trying again:
smoothing of 120, avoid_vent -1
Warning 3dSkullStrip: Stubborn intersection remaining at smoothing of 120. Ignoring it.The intensity in the output dataset is a modified version
of the intensity in the input volume.
To obtain a masked version of the input with identical values inside
the brain, you can either use 3dSkullStrip's -orig_vol option
or run the following command:
3dcalc -a ./CI_001_M4.anat+orig -b ./CI_001_M4.anat_ns+orig -expr 'a*step(b)' \
-prefix ./CI_001_M4.anat_ns_orig_vol
to generate a new masked version of the input.
Resampling ...
invalid master dataset <__ats_tmp__ref_MNI152_T1_2009c_CI_001_M4_40pad+tlrc>
Failed to resample

I am confused because I thought I had copied everything correctly and the only thing I really changed was the parent auto_tlrc file, which should be an exact copy of what I used to use. What am I doing wrong and how can I fix it?

I am running:
Ubuntu version 14.04, AFNI Precompiled binary linux_openmp_64: Aug 28 2018 (Version AFNI_18.2.15)

Thanks!