Hi,
you should co register your structural scans with robust-register or
robust-template (if you have more than 2). This can be done into the
midspace to make sure both time points are mapped to avoid processing bias.
You can then register the functional scans to their corresponding
structurals and concat the transforms to get everything into the same
midspace.
Best, Martin
On 02/10/2016 12:48 PM, Ji Won Bang wrote:
Dear. Freesurfer team.
Thanks so much your help and advice.
Based on the comments, I'm trying freesurfer version 5.3.0 instead of
4.5.0 now.
In our experiment, each participant is scanned twice on different days
and the functional scan's brain volume are different (some scans have
33 number of slices, some have 32 number of slices).
Since participants moved a bit between scans on the same day, and the
head position is different between different days, my advisor advised
me to do co-registration between different functional scans and then
do co-registration between anatomical and functional scans.
My question is this.
If I do motion-correction such that we align all EPI data to the first
EPI of the first functional scan, will it be enough for
co-registration between different functional scans and different days?
Or should I do coregistration-specific process such as
mri_robust_register, mri_robust_template etc?
Or I guess the method I choose should depend on how much the
participant moved between scans and how much different the head
position was between different days? For example, if the participant
was very still between runs and the head position was not that too
different, this motion correction is enough for coregistration between
functional scans. However, if not, I should do coregistration-specific
process such as mri_robust_register, mri_robust_template etc?
I'd appreciate any of your advice.
Please feel free to let me know your thoughts.
Best,
Ji Won
2016-02-08 22:31 GMT-05:00 Douglas Greve <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>:
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 <kirsten...@gmail.com
<mailto: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
<mailto: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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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
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contains patient information, please contact the Partners Compliance HelpLine at
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