External Email - Use Caution
Thank you for your response. Just to clarify, the first command should be mri_vol2surf, correct? It appears to have worked; however, I'm not sure what my --trgsurfval should be? I'm trying the following commands, where mni is the subject directory for the mni brain I recon-ed and sub01 is the subject I want to transfer the atlas to so that I can obtain the cortical thickness.
1. mri_vol2surf --mov atlas.nii.gz --regheader mni --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz
2. mri_surf2surf --srcsubject mni --srcsurfval lh.atlas.nii.gz --trgsubject sub01 --trgsurfval hammers-01-lh.img --mapmethod nnf
I tried running mri_surf2surf --help, but unfortunately the examples didn’t really apply to my case. I apologize for the potential trivial question in advance. Thanks again for your help.
Best,
Ryan
--
Ryan Flores
Clinical Research Coordinator
On 6/14/18, 8:33 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote:
You can always get info by running the command with --help.
mri_vol2vol --mov atlas.nii.gz --regheader subject --hemi lh
--projfrac-max 0 1 .1 --o lh.atlas.nii.gz
This assumes that the atlas is in registration with the mni152 (you can
test with tkregister --mov atlas.nii.gz --s subject --regheader --reg
deleteme.dat, the two volumes should be in registration)
You can take lh.atlas.nii.gz and use it as input to mri_surf2surf to
transfer to an individual. Make sure to use --mapmethod nnf
On 06/13/2018 06:59 PM, Ryan Flores wrote:
>
> External Email - Use Caution
>
> Hello all,
>
> I am hoping to obtain structural information (e.g., cortical
> thickness, surface area, and volume) based on the n30r83 (aka
> Hammersmith) atlas, which is in MNI space. The atlas differentiates
> between the hemispheres by using odd/even numbers in the labels.
>
> After looking through the archives I found a potential solution, which
> entails using the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed
> the MNI brain to obtain the proper space; however, I’m unsure of how
> exactly to implement the commands and which flags are relevant. Any
> advice would be greatly appreciated.
>
> Thank you for your time. I look forward to hearing from you.
>
> Best,
>
> Ryan
>
> --
>
> Ryan Flores
>
> Clinical Research Coordinator
>
>
>
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