External Email - Use Caution 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 <dgr...@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.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 >> > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
