What is the "MNI template" that you are using. I mean an exact file used. Did you use this file when you ran recon-all?
On 04/12/2018 10:23 AM, srishti goel wrote: > Yeah, I am unsure where to go from here as well. So the results can be > viewed in SPM and on the MNI template space itself, since SPM > typically does not have a problem showing multiple images in different > sizes. > > 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 12, 2018 at 10:11 AM, Douglas N. Greve > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > 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> <mailto: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> > <mailto: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> <mailto: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> > <mailto: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> > >>> <mailto: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> > <mailto: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> > >>>> <mailto: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> > >>>>> <mailto: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> > >>>>> <mailto: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> > >>>>> <mailto: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> > >>>>> <mailto: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> > >>>>> <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. 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