11 Apr
2018
11 Apr
'18
11:30 p.m.
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): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@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): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve <dgreve@mgh.harvard.edu <mailto:dgreve@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 <23srishtigoel@gmail.com <mailto:23srishtigoel@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): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@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): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@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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