Re: [Freesurfer] Get Atlas surfaces in subject space

[Douglas N. Greve]

You should load the surfaces in FV. If it load in FV ok but nibable is 
crashing, you should contact them.

On 5/5/2020 1:05 PM, Ian Hardingham wrote:

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Thank you both.

I've made edits and these are the current commands:

mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_lh.white
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_rh.white
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_lh.pial
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_rh.pial

These execute successfully and the file size looks about right, but 
after using mris_convert to convert to Gifti format nibabel crashes on 
trying to load them - is there anything obviously wrong in my commands?

I'll also take a look at mris_apply_reg.

On 05/05/2020 18:01, Douglas N. Greve wrote:
Don't specify a --trg_type. But add --tval-xyz
mris_apply_reg will do the same thing, but the interface might be a 
little easier

On 5/5/2020 12:49 PM, Bruce Fischl wrote:
no definitely not "w" format, which we don't use for anything 
anymore. YOu should use tval-xyz also I think
On Tue, 5 May 2020, Ian Hardingham wrote:


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It would appear not, as I'm getting an error on my pial output 
files but not
my white ones.  Here are my commands:

mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white 
--trgsubject
fs_target --trgsurfval ./registered_lh.white --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white 
--trgsubject
fs_target --trgsurfval ./registered_rh.white --trg_type w
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial 
--trgsubject
fs_target --trgsurfval ./registered_lh.pial --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial 
--trgsubject
fs_target --trgsurfval ./registered_rh.pial --trg_type w

The white calls output seems to be fine, but the pial ones aren't.  I
somewhat naively trued trg_type pial but that wasn't correct.

On 05/05/2020 17:33, Ian Hardingham wrote:

      Thanks Bruce, extremely helpful.

      Can I just check that the "w" format is what is used by both the
      lh/rh.pial and the lh/rh.white files?  I only ask because my
      surf2surf command outputs the exact output filename if the end
      is ".white", but if it's ".pial" it outputs ".pial.w", which I
      find a little curious.

      Ian

      On 05/05/2020 16:34, Bruce Fischl wrote:
      yes, check out options like:
      --sval-xyz

      if you need further help though I'll have to defer to Doug
      :)
      Bruce


      On Tue, 5 May 2020, Ian Hardingham wrote:


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            Bruce, I've read the docs on mri_surf2surf - I
            wish to get surface files out
            (again, lh.pial, rh.pial, lh.white, and
            rh.white) rather than values for
            something such as thickness - is there an
            option for mri_surf2surf to allow
            this?

            On 05/05/2020 14:43, Bruce Fischl wrote:
                  Hi Ian

                  you can use mri_surf2surf to map
            surfaces between subjects, but
                  our atlas isn't really a surface. You
            can use the surfaces in
                  the fsaverage dir, but they are meant
            for visualization and are
                  much smoother than individuals

                  cheers
                  Bruce


                  On Tue, 5 May 2020, Ian wrote:


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            Caution

                        Hi Freesurfers.

                        I have a subject S with recon-all
            having been run on
                        it.

                        I have the subject-specific
            surface files
                        /surf/lh.pial, rh.pial, lh.white,
                        and rh.white.

                        I would like an Atlas's lh.pial,
            rh.pial, lh.white,
                        and rh.white in subject
                        space.

                        Any helpers on how to achieve
            this?

                        Thanks,
                        Ian

                        --

                        Ian Hardingham





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