I'm guessing that AFNI can't do MC on a 2d "volume" (MC is inherently a 3D operation). You can try turning off MC in preproc-sess with -nomc

On 9/25/2020 11:56 AM, Nasr, Shahin,Ph.D. wrote:

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