12 Apr
2018
12 Apr
'18
10:23 a.m.
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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 12, 2018 at 10:11 AM, Douglas N. Greve dgreve@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): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@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): 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 specifythe
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 findmni152_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! > > > > ______________________________
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