can you run mris_info on the output surfcae? And maybe send a freeview snapshot of it (in 3d rendering mode)
On Wed, 6 May 2020, Ian wrote:
External Email - Use CautionThanks 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:
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
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