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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