It might be the initialization with FLIRT. Do you have access to FS6.0?
If so, can you try running 6.0 instead to see if it fixes the problem?
On 5/14/18 4:05 AM, Patrycja Naumczyk wrote:
Hi All,
I'm still struggling with the registration - so far I tried performing
slice-timing and/or motion correction in SPM instead of FS, but that
did not changed the results.
I came up with a new idea, but don't know how to verify it. I used GE
scanner for data acquisition, which meant I had to convert the fMRI
data and make the directory tree myself (as the dcm-unpack did not
work well). I used MRIconvert for converting to nifti, which does not
preserve some of the FS-Fast crucial data (i.e. the TR, which I had to
update with mri_convert in all files). Is it possible that this is the
reason of bbregister's misalignment? Like, the script needs some
additional information that should be embedded in the data and is not
(due to outside conversion)?
I was thinking of maybe working around the problem by manually
registering the rs-fMRI template to task-based template and then
merging the two registration files (rs-fMRI_to_taskBased and
taskBased_to_anatomical) and feeding that to the preproc-sess with
"-regfile" flag. Potentially it could work, but maybe there is a
simpler solution?
The only difference between the properly aligned task-based fMRI and
faulty rs-fMRI is that the latter has lower resolution (task based:
2.5x2.5x3.2mm, rs-fMRI: 3.4x3.4x3.3mm) and was longer (task-based: 160
volumes, rs-fMRI: 400 volumes).
I attach screenshot of the problem in tkregister. Left - task-based
fMRI, middle - rs-fMRI, right - rs-fMRI with task-based registration
file used.
Best regards,
Patrycja
2018-05-12 15:20 GMT+02:00 Patrycja Naumczyk
<patrycja.naumc...@gmail.com <mailto:patrycja.naumc...@gmail.com>>:
Hi All,
I'm running FS v. 5.3 on Gentoo Linux.
I made a study, where all subjects during one session had T1,
resting-state and task-based fMRI. I processed all anatomical data
through standard recon-all (it worked well), and the task-based
fMRI through FS-FAST - which also generated fine results.
Now I wanted to look into the rs-fMRI with functional
connectivity. I made a separate directory tree for this purpose
(in order not to mess task and rest data), and unfortunately the
bbregister doesn't handle the registration during preproc-sess
properly. Misalignment is big and covers all runs. BBR-sums of all
of participants (N=39) exceed 0.8 (some of them exceed 1.0).
What's interesting is that bbregister previously managed the
task-based fMRI data well (with no BBR-sum exceeding 0.8). I
double checked the data for any i.e. conversion/orientation
faults, but found none.
The command for preprocessing was identical in rs-fMRI and
task-based fMRI:
preproc-sess -sf <sessid> -d <ProjectDirectory> -surface fsaverage
lhrh -mni305 -fwhm 5 -per-run -fsd bold
I attach exemplary register log file from rs-fMRI subject
registration (BBRsum=0.9704). This subject's task-based fMRI
BBR-sum was 0.55.
My question is - what may be the cause of such a discrepancy
between registration of two functional runs taken one by one (the
rs-fMRI preceded the task based)? Does anyone have an idea how to
fix the problem?
Best regards,
Patrycja
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