21 May
2018
21 May
'18
11:42 a.m.
The problem appears to be that your data are not really T2* weighted in that the intensity of cortex (about 830) is less than that of WM (about 862). Try running preproc-sess with -t1 to indicate to bbregister that your data are t1 weighted.
On 05/17/2018 03:57 AM, Patrycja Naumczyk wrote:
I did not receive an email previously - it occurred I misspelled your e-mail address. I uploaded the files again, this time with an email confirmation so it should be working now. My apologies, Patrycja
2018-05-17 2:52 GMT+02:00 Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:
I did not get it. You should have gotten an email. Can you forward it to me? On 5/16/18 6:50 AM, Patrycja Naumczyk wrote:could please confirm receiving the files I sent the other day? By any chance, maybe You had a time to look into them? Best regards, Patrycja 2018-05-14 20:01 GMT+02:00 Patrycja Naumczyk <patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>>: OK - the 5.3 or the 6.0 version? 2018-05-14 20:00 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu <mailto: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> > <mailto: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> <mailto: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 >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto: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> >> <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:Freesurfer@nmr.mgh.harvard.edu> <mailto: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> > <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> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . 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Douglas N. Greve