In 4.5 I don't think there is a way to run it when different runs have different number of slices. Version 5+ will handle it properly. If you really want to use 4.5, then you'll have to put it in a different functional subdir (FSD, eg, bold), and create a new analysis for it, then combine them together after analysis. A bit of a hassle.

On 2/8/16 5:58 PM, Ji Won Bang wrote:
Dear. Freesurfer team.

As another attempt, I run the motion correction without the argument -targrun:

mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino

However, I get the same error message again.

Why is that?

Thanks so much for your effort and time.

I appreciate it a lot.

Best,
Ji Won


2016-02-08 17:16 GMT-05:00 Ji Won Bang <kirstens03@gmail.com>:
Dear. Freesurfer team.

I'd appreciate any advice from you.

When doing the motion correction, I'd like to align all EPI data(bold_retino) to the first EPI of target run(bold_decode/003). However, the number of slices for target run(33) and the number of slices(32) for input run(bold_retino) are different. 

When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003

Freesurfer says that:
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
Invalid null command.
These two kinds of run (bold_decode, bold_retino) were collected in one scan per subject, so the head position should not be too different...

Do you have any suggestions for fixing this error?

Should I do 3dWarp -deoblique? 

Thank you so much.

Best,
Ji Won 

2016-02-08 16:30 GMT-05:00 Ji Won Bang <kirstens03@gmail.com>:
Dear. Freesurfer team.

Hi.

I'm using freesurfer 4.5 version.

While doing the motion correction, an error occurred.

the command I used:
mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003

the error I have:
/home/jbang/Projects/replay/epi/replay01/bold_retino
3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
++ Authored by: RW Cox
*+ WARNING:   If you are performing spatial transformations on an oblique dset,
  such as 025/tmp.mc-afni2.32291/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:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb.
++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz
++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb.
++ centers of base and input datasets are 9.09 mm apart
** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions!
   Input: nx=74  ny=74  nz=32
   Base:  nx=74  ny=74  nz=33
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
Invalid null command.

I think it's because the volume size is different.

The volume size for bold_retino is: number of slices 32
The volume size for bold_decode: number of slices 33

What should I do to correct this error?

Thank you for taking your time.

Best,
Ji Won




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