Hi Surfers,

     I have faced an issue with preproc-sess and I appreciate your help.  I have a single slice EPI scan (number of TRs > 500; TR=0.2). When I tried to do preproc-sess,  mc-afni2 is called and it crashed.  When I checked the log, I noticed this:

3dvolreg.afni -verbose -dfile 005/fmcpr.mcdat -1Dmatrix_save 005/fmcpr.mat -base 005/tmp.mc-afni2.4869/tempvol.nii.gz -prefix 005/tmp.mc-afni2.4869/outvol.nii.gz 005/tmp.mc-afni2.4869/invol.nii.gz

++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit]

++ Authored by: RW Cox

*+ WARNING:   If you are performing spatial transformations on an oblique dset,

  such as 005/tmp.mc-afni2.4869/tempvol.nii.gz,

  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:005/tmp.mc-afni2.4869/tempvol.nii.gz is 30.100002 degrees from plumb.

++ Reading in base dataset 005/tmp.mc-afni2.4869/tempvol.nii.gz

++ Oblique dataset:005/tmp.mc-afni2.4869/invol.nii.gz is 30.100002 degrees from plumb.

++ Reading input dataset 005/tmp.mc-afni2.4869/invol.nii.gz

++ Edging: x=3 y=3 z=0

++ Creating mask for -maxdisp

 + Automask has 847 voxels

 + 847 voxels left in -maxdisp mask after erosion

++ Initializing alignment base

*** mri_3dalign_setup: cannot use nD images!

** Can't initialize base image for alignment

ERROR: 3dvolreg.afni

Invalid null command.

Any suggestions?

Please note that, this data is properly registered (manually and based on an auxiliary volume) and there is no problem there.

Regards