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 mailto: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 <mailto: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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