Hi,
I tried using bbregister to register my files with the following command:
bbregister --mov negative_allsocial.nii --bold --s SN_like_cortical_lh.gz --init-rr --lta register.lta
and this is the error I received:
reading source './tmp.bbregister.173331/template.nii'...
mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.173331/template.nii.
No such file or directory
I would like to re-iterate my issue as that might be helpful. We have carried out a meta analysis and want to compare our meta analytic maps to someone's else's map. Our meta analytic map is negative_allsocial.vmp which we converted to a nifti using neuroelf and now have the negative_allsocial.nii. We want to see how someone else's map which is the SN_like_cortical_lh.gz (they said to view this on a subject file to which they gave us the link) compares to our map. We would also further want to see how our map compares to their volume map which is SN_like_subcortical.nii (these are in MNI152 volume space). We are using mri_vol2surf to view compare the two files.
mri_vol2surf --src negative_allsocial_proportion.nii --src_type analyze --srcreg [REGISTRATION MATRIX] --hemi lh --o ./neg_allsocial.nii --projfrac 0.5
And for the registration matrix I tried using bbregister as told my the freeSurfer help group.
I can send the files as well if required and would highly appreciate some prompt help on this.
Thanks so much!
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 skype: srishti.goel12
On Fri, Mar 9, 2018 at 11:15 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
You create it with bbregister. See the multimodal integration tutorial
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview
On 3/6/18 6:36 PM, srishti goel wrote:
I am sorry but that is what I am unsure about it. I don't know how to obtain a registration matrix or which registration matrix to use for this.
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 Mon, Mar 5, 2018 at 3:24 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Why did you remove the registration file? --srcreg below
On 02/28/2018 04:13 PM, srishti goel wrote:
Hello,
Thank you so much! I used the following command as you said and got an error : must specify a source registration file or --regheader
mri_vol2surf --src negative_allsocial_avgnull.nii --src_type analyze --trgsubject fsaverage --hemi lh --o ./neg_allsocial.nii --projfrac 0.5
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, Feb 28, 2018 at 10:13 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
you need to add --trgsubject fsaverage to your mri_vol2surf command line On 2/27/18 12:23 PM, srishti goel wrote:Hello, We are trying to project a volume map onto a surface. Our network based volume map is a .vmp file and our surface is a nifti file. We were able to convert the volume maps from .vmp to nifti. Our volume map is: negative_allsocial_proportion.nii Our surface is: SN_like_cortical_lh.nii The output file is named: neg_allsocial.nii We are trying to use the following command to now project the volume map on surface and the issues we are facing are: 1) We are unsure of what the purpose of the registration file is and where in the mir_vol2surf command should we specify the surface 2) If it is a matrix for something related to the surface on which we want to project our volume then how should we go about obtaining the registration file appropriate for our comparison. _Command:_ mri_vol2surf --src negative_allsocial_proportion.nii --src_type analyze --srcreg [REGISTRATION MATRIX] --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 _Then to project it:_ tksurfer fsaverage lh inflated -ov neg_allsocail.nii _______________________________________________ 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>
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