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 <kirsten...@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 <kirsten...@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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