2018-05-14 20:00 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu>:

Can you tar up one of your subjects (fmri and FS analysis) and send it
to me on our file drop below?

On 05/14/2018 01:58 PM, Patrycja Naumczyk wrote:
>
>
> Hi Doug,
>
> we have v.6.0 on a cluster, so I quickly run one subject there (the
> one, whose files and pictures I attached previously). This time the
> BBR-sum was 0.9476, so slightly better but still bad :(
>
> Best regards,
> Patrycja
>
> 2018-05-14 16:56 GMT+02:00 Douglas Greve <dgreve@mgh.harvard.edu
> <mailto:dgreve@mgh.harvard.edu>>:

>
> 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.naumczyk@gmail.com <mailto:patrycja.naumczyk@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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