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" <dgr...@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: > > > > External Email - Use Caution > > > > 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: > >>> > >>>> > >>>> External Email - Use Caution > >>>> > >>>> 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: > >>>> > >>>> > >>>> External Email - Use Caution > >>>> > >>>> 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: > >>>> > >>>> > >>>> External Email - Use > >>>> 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 > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
