Hi again,

I was able to get the script to run through to the end without stalling, but I am receiving a lot of errors during the @auto_tlrc process, so I am unsure if the received outputs are correct.

I looked through the @auto_tlrc documentation but I'm not sure what the problem might be. Would you be able to look at some of these messages and help me identify if they are an issue? Particularly I am unsure how to handle these messages or if they should be of concern:

ans: Subscript out of range.
*** Can't open dataset MNI152_1mm_uni+tlrc
v1_center_RAI: Subscript out of range.

williamss@linux5% /data/nil-external/ccp/OASES/OASES_FMRI/atlas/@toMNI_Awarp awarp5 205_MPRAGE_strip+orig.HEAD 206_MPRAGE_strip+orig.HEAD
mkdir: created directory `awarp5'

===== @toMNI_Awarp: copying input datasets to awarp5 =====

++ 3dcopy: AFNI version=AFNI_17.2.09 (Aug 22 2017) [64-bit]
++ 3dcopy: AFNI version=AFNI_17.2.09 (Aug 22 2017) [64-bit]

===== @toMNI_Awarp: beginning 3dUnifize loop =====

mkdir: created directory `Temp1'
++ 3dUnifize: AFNI version=AFNI_17.2.09 (Aug 22 2017) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./205_MPRAGE_strip+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./205_MPRAGE_strip+orig.BRIK is 11.389321 degrees from plumb.
+ Pre-processing: ADV....UWG
++ ===== Elapsed = 55.0 sec
mkdir: created directory `Temp2'
++ 3dUnifize: AFNI version=AFNI_17.2.09 (Aug 22 2017) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./206_MPRAGE_strip+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./206_MPRAGE_strip+orig.BRIK is 8.574255 degrees from plumb.
+ Pre-processing: ADV....UWG
++ ===== Elapsed = 52.6 sec

===== @toMNI_Awarp: beginning @auto_tlrc loop =====

ans: Subscript out of range.
*** Can't open dataset MNI152_1mm_uni+tlrc
v1_center_RAI: Subscript out of range.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./205_MPRAGE_strip_uni+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./205_MPRAGE_strip_uni+orig.BRIK is 11.389321 degrees from plumb.
c1: Subscript out of range.
Center distance of mm no auto_center needed
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./205_MPRAGE_strip_uni+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./205_MPRAGE_strip_uni+orig.BRIK is 11.389321 degrees from plumb.
ans: Subscript out of range.
*** Can't open dataset MNI152_1mm_uni+tlrc
v1_center_RAI: Subscript out of range.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./205_MPRAGE_strip_uni+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./205_MPRAGE_strip_uni+orig.BRIK is 11.389321 degrees from plumb.
c1: Subscript out of range.
Center distance of mm
Padding ...
++ 3dZeropad: AFNI version=AFNI_17.2.09 (Aug 22 2017) [64-bit]
** 3dZeropad: Can't open dataset MNI152_1mm_uni+tlrc
Failed to pad
ans: Subscript out of range.
*** Can't open dataset MNI152_1mm_uni+tlrc
v1_center_RAI: Subscript out of range.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./206_MPRAGE_strip_uni+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./206_MPRAGE_strip_uni+orig.BRIK is 8.574255 degrees from plumb.
c1: Subscript out of range.
Center distance of mm no auto_center needed
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./206_MPRAGE_strip_uni+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./206_MPRAGE_strip_uni+orig.BRIK is 8.574255 degrees from plumb.
ans: Subscript out of range.
*** Can't open dataset MNI152_1mm_uni+tlrc
v1_center_RAI: Subscript out of range.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./206_MPRAGE_strip_uni+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./206_MPRAGE_strip_uni+orig.BRIK is 8.574255 degrees from plumb.
c1: Subscript out of range.
Center distance of mm
Padding ...
++ 3dZeropad: AFNI version=AFNI_17.2.09 (Aug 22 2017) [64-bit]
** 3dZeropad: Can't open dataset MNI152_1mm_uni+tlrc
Failed to pad
mv: will not overwrite just-created `./MNI152_1mm_uni+tlrc.BRIK' with `Temp2/MNI152_1mm_uni+tlrc.BRIK'
mv: will not overwrite just-created `./MNI152_1mm_uni+tlrc.HEAD' with `Temp2/MNI152_1mm_uni+tlrc.HEAD'

===== @toMNI_Awarp compressing output BRIK files =====

205_MPRAGE_strip+orig.BRIK: 90.4% -- replaced with 205_MPRAGE_strip+orig.BRIK.gz
206_MPRAGE_strip+orig.BRIK: 90.6% -- replaced with 206_MPRAGE_strip+orig.BRIK.gz
MNI152_1mm_uni+tlrc.BRIK: 78.4% -- replaced with MNI152_1mm_uni+tlrc.BRIK.gz

===== @toMNI_Awarp is wrapped up, done, finished, and over =====


Thanks so much for your help

Best,
Sam Williams