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Thanks Tim and Doug.

I have the files generating and loading properly now, but I'm not convinced it's giving the output I'm looking for.

I am trying to convert the "fsaverage" subject's surface coordinates to my own subject's surface space.

FSaverage's lh.white file is 5898808 bytes:

5898808 Apr 11  2013 /usr/local/freesurfer/subjects/fsaverage/surf/lh.white

After converting with this command:

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

My newly registered lh.white file is half the size:

3316997 May  6 10:41 /home/ian/cdm_registered_test/registered_lh.white

(and appears to have half the vertices accordingly.)

So this must be incorrect, or at least not my intended purpose.

To try and be clear, I'm looking to get the position of every vertex in fsaverage's surfaces "on" the surface of my subject's surfaces.  So if there's a vertex at the peak of a particular sulcii on fsaverage, I'm looking to find where the peak of that sulcii is on my subject.

Thanks,
Ian

        External Email - Use Caution        

Just a note: there should be no need to convert to gifti, nibabel can read the FreeSurer binary surface format directly with `nibabel.freesurfer.io.read_geometry()`.

The docs are here: https://nipy.org/nibabel/reference/nibabel.freesurfer.html#nibabel.freesurfer.io.read_geometry

Best,

Tim

On May 5, 2020 at 7:59 PM "Douglas N. Greve" <dgreve@mgh.harvard.edu> wrote:


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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                        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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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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