External Email - Use Caution OK - the 5.3 or the 6.0 version?
2018-05-14 20:00 GMT+02:00 Douglas N. Greve <dgr...@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 <dgr...@mgh.harvard.edu > > <mailto: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 <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 > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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