When you use bbregister, it is expecting the input nii file to represent the actual anatomy of the subject, so it does not surprise me that it does not work that well. I'm not sure what to do about this because a meta analysis image will never have decent anatomy. In theory, it should be already in alignment with the mni152, but this is trickier than it seems. How do you usually view the results? In FSL or SPM? Do you view them on an anatomical image?
On 04/12/2018 09:03 AM, srishti goel wrote: > Hi Douglas, > > The negative_allsocial_proportion.nii file has actually been converted > from a vmp file - 'negative_allsocial.vmp'. We used neruoelf to > convert the vmp file, option - 'export to analze' and 'export to > nifti'. The original vmp file represent the results of a meta-analysis. > > Let me know if that helps or you would need more information. > > Thanks! > > Best, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> > skype: srishti.goel12 > > > On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > how was negative_allsocial_proportion.nii created? > > > On 4/11/18 9:14 PM, srishti goel wrote: >> Hi, >> >> I used bbregister to register: >> bbregister --mov negative_allsocial_proportion.nii --s >> mni152_subject --bold --lta register.lta >> and then viewed it using: >> tkregisterfv --mov negative_allsocial_proportion.nii --reg >> register.lta --surfs >> It doesn't look great but it still looks okay (Screenshot attached). >> Then I also used lta in tkregisterfv, as: >> tkregisterfv --mov negative_allsocial_proportion.nii --reg >> register.lta --s mni152_subject --surfs --reg reg.deleteme.dat >> In this file, the volume map still lies outside the surface. >> Could you please help me resolve this issue. >> I tried using register.lta file in the mri_vol2surf but the >> overlay map doesn't show up again. >> Thanks! >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu> >> skype: srishti.goel12 >> >> >> On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve >> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: >> >> don't use --init-rr ( you don't need to spec an init in >> version 6) >> >> >> On 4/10/18 9:48 PM, srishti goel wrote: >>> When I run bbregister, it gives me an error. Attached is the >>> register.dat.log file for it. >>> Error: >>> >>> reading source './tmp.bbregister.91068/template.nii'... >>> >>> mri_robust_register.bin: only pass single frame MRI source >>> ./tmp.bbregister.91068/template.nii. >>> >>> >>> No such file or directory >>> >>> >>> Any help is greatly appreciated! >>> >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> <mailto:srish...@email.unc.edu> >>> skype: srishti.goel12 >>> >>> >>> On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve >>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: >>> >>> They are not in registration. Try running bbregister to >>> create a registration file (lta), then pass the lta to >>> tkregisterfv instead of --regheader >>> >>> >>> On 4/9/18 11:49 PM, Bruce Fischl wrote: >>>> How did you generate the registration? And give us the >>>> details of what you are trying to register >>>> Cheers >>>> Bruce >>>> >>>> On Apr 8, 2018, at 2:55 PM, srishti goel >>>> <23srishtig...@gmail.com >>>> <mailto:23srishtig...@gmail.com>> wrote: >>>> >>>>> Hi Bruce, >>>>> >>>>> Thanks so much for pointing that out, I totally missed >>>>> that part. >>>>> >>>>> Also, the registration definitely isn't appropriate. >>>>> Could someone please guide me how to correct this >>>>> problem. I have attached a screenshot of how it looks >>>>> like currently. >>>>> >>>>> >>>>> <Screen Shot 2018-04-08 at 2.53.33 PM.png> >>>>> >>>>> Best, >>>>> Srishti >>>>> Social/Clinical Research Specialist >>>>> Child Imaging Research and Life Experiences Lab >>>>> University of North Carolina at Chapel Hill >>>>> email (W): srish...@email.unc.edu >>>>> <mailto:srish...@email.unc.edu> >>>>> skype: srishti.goel12 >>>>> >>>>> >>>>> On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl >>>>> <fis...@nmr.mgh.harvard.edu >>>>> <mailto:fis...@nmr.mgh.harvard.edu>> wrote: >>>>> >>>>> Hi Srishti >>>>> >>>>> the directory you are in doesn't matter. YOu >>>>> either need to set SUBJECTS_DIR in the >>>>> environment, or use --sd <SUBJECTS_DIR> to specify the >>>>> directory that contains your subjects. I think you >>>>> can also give it the full path to a target volume >>>>> if you want, but maybe Doug can comment as he >>>>> knows this stuff better than I do >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> >>>>> On Sun, 8 Apr 2018, srishti goel wrote: >>>>> >>>>> When I type this command:tkregisterfv --mov >>>>> negative_allsocial_proportion.nii --regheader --s >>>>> mni152_subject --surfs --reg reg.deleteme.dat >>>>> >>>>> It gives me the error: cannot find mni152_subject. >>>>> Although I clearly checked that the directory >>>>> from which I am submitting this command has the >>>>> mni152_subject directory within which there >>>>> are all the other required directories such >>>>> as: mri, >>>>> stats, surf, scripts, etc. >>>>> >>>>> I am unsure what is happening here. >>>>> >>>>> >>>>> Best, >>>>> Srishti >>>>> Social/Clinical Research Specialist >>>>> Child Imaging Research and Life Experiences Lab >>>>> University of North Carolina at Chapel Hill >>>>> email (W): srish...@email.unc.edu >>>>> <mailto:srish...@email.unc.edu> >>>>> skype: srishti.goel12 >>>>> >>>>> >>>>> On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. >>>>> Greve <dgr...@mgh.harvard.edu >>>>> <mailto:dgr...@mgh.harvard.edu>> wrote: >>>>> Those commands look ok. My suspicion >>>>> goes to the use of --regheader. See >>>>> whether the registration is ok with >>>>> >>>>> tkregisterfv --mov >>>>> negative_allsocial_proportion.nii --regheader --s >>>>> mni152_subject --surfs --reg reg.deleteme.dat >>>>> >>>>> >>>>> On 04/05/2018 08:34 AM, srishti goel wrote: >>>>> > Hi, >>>>> > >>>>> > I am trying to compare my volume maps >>>>> > (negative_allsocial_proportion.nii) to >>>>> someone else's >>>>> > (SN_like_cortical_lh.nii.gz) who have >>>>> it on a surface >>>>> > (mni152_subject). So I used the steps >>>>> for mri_vol2surf command as >>>>> > follows: >>>>> > >>>>> > Commands: >>>>> > mri_vol2surf --src >>>>> negative_allsocial_proportion.nii --regheader >>>>> > mni152_subject --hemi lh --o >>>>> ./neg_allsocial_lh.nii --projfrac 0.5 >>>>> > Then to view it: >>>>> > tksurfer mni152_subject lh inflated >>>>> -overlay ./neg_allsocial_lh.nii >>>>> > -overlay SN_like_cortical_lh.nii.gz >>>>> -fthresh 0.5 >>>>> > >>>>> > Everything ran fine and we didn't get >>>>> any error but then while viewing >>>>> > the files we could not see our map >>>>> (neg_allsocail_lh.nii) on the >>>>> > surface. This file seemed to work fine >>>>> as it is not an empty file when >>>>> > I checked the file size. However, when >>>>> we view it using tksurfer it >>>>> > does not show up as a highlighted >>>>> portion on the surface. The >>>>> > SN_like_cortical_lh.nii.gz file shows >>>>> up just fine. >>>>> > >>>>> > Could someone please help me figure >>>>> out what might have gone wrong here. >>>>> > >>>>> > Thanks so much! >>>>> > >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > 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:Freesurfer@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. 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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 >>>>> <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: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:Freesurfer@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 >>> <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:Freesurfer@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 >> <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:Freesurfer@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
