Hi Bruce,Thank you for the response.
Maryam
On Friday, April 29, 2016 1:54 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Maryam
I think it would be
foreach hemi (lh rh)
mris_make_surfaces -whiteonly -mgz \
-T1 ${hemi}.brain.finalsurfs <subject ID> $henmi
mris_make_surfaces -nowhite -orig_pial white
-T1 ${hemi}.brain.finalsurfs <subject ID> $henmi
if you want, you can also use -output .test and it will add .test to all
the output names so you can see the effect of your edits
cheers
Bruce
On Fri, 29 Apr 2016, maryam koochaki wrote:
> Dear experts,I am trying to fix the surfaces which are crossing to each
> other in the middle where the hemispheres reach each other.
> As Bruce mentioned before I am trying to create two volumes
> (lh.brain.finalsurfs.mgz , rh.brain.finalsurfs.mgz ) nad edit them
> individually.
> Then I want to rerun this command for each hemi:
> mris_make_surfaces -subjid <name> -whiteonly -noaparc -mgz -T1
> lh.brain.finalsurfs lh
>
> mris_make_surfaces -subjid <name> -white NOWRITE -mgz -T1
> lh.brain.finalsurfs lh
>
> Am I using the correct command?
> What should I expect to have after running this command line(for example
> first one)?
> Sould I rerun (recon-all -autorecon-pial ) after all?
>
> Thanks in advance for the help,
>
> Maryam
>
>
>
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