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