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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
On 06/05/2020 09:08, Tim Schäfer wrote:
External Email - Use CautionJust 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.freesurfe...
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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