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
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
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
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
External Email - Use Caution
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
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
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
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
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
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
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.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
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
External Email - Use Caution
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:
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
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
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
External Email - Use Caution
FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines?
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-0.9990, -0.0436, 0.0000) y_(ras) : (-0.0436, 0.9990, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.00000 92.25847; -0.04362 0.99905 0.00000 -99.12585; 0.00000 0.00000 1.00000 -145.07230; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 88.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 112.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talairach_flag 0 rescale 0.000000 nvertices 102020 nfaces 204036 total_area 65520.492188 group_avg_vtxarea_loaded 0 avgvtxarea 0.642232 avgvtxdist 0.940503 stdvtxdist 0.417776 vtx0xyz -8.576451 -101.319672 3.333434
On 06/05/2020 15:00, Bruce Fischl wrote:
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 Caution 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 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.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
_______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hmm, that is not an icosahedral surface, which should have 160K vertices. Can you check your input surface? You'll also need to fix your freeview problem, but someone else will have to help you with that On Wed, 6 May 2020, Ian Hardingham wrote:
External Email - Use Caution
FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines?
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-0.9990, -0.0436, 0.0000) y_(ras) : (-0.0436, 0.9990, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.00000 92.25847; -0.04362 0.99905 0.00000 -99.12585; 0.00000 0.00000 1.00000 -145.07230; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 88.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 112.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talairach_flag 0 rescale 0.000000 nvertices 102020 nfaces 204036 total_area 65520.492188 group_avg_vtxarea_loaded 0 avgvtxarea 0.642232 avgvtxdist 0.940503 stdvtxdist 0.417776 vtx0xyz -8.576451 -101.319672 3.333434
On 06/05/2020 15:00, Bruce Fischl wrote: 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 Caution 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 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.freesur fer.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: 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks Bruce.
So a reminder I'm calling:
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
I'm assuming that means the "input surface" is /usr/local/freesurfer/subjects/fsaverage/surf/lh.white, and here's the mris_info for that, but bear in mind that I don't know for sure from that line that that's what is being used.
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 163842 num faces : 327680 num strips : 0 surface area: 65417 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 group avg surface area: 82220 ctr : (-31.9282, -18.8144, 16.3699) vertex locs : surfaceRAS talairch.xfm: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; surfaceRAS to talaraiched surfaceRAS: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; talairached surfaceRAS to surfaceRAS: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Volume Geometry (vg) volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 0.0000, 0.0000, 0.0000) file : ../mri/orig.mgz Volume Geometry vox2ras -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mris_info creationtime 2020/05/06-14:31:38-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /usr/local/freesurfer/subjects/fsaverage/surf/lh.white hemicode 0 talairach_flag 0 rescale 0.000000 nvertices 163842 nfaces 327680 total_area 65416.984375 group_avg_surf_area 82219.960938 group_avg_vtxarea_loaded 1 avgvtxarea 0.399269 avgvtxdist 0.721953 stdvtxdist 0.195470 vtx0xyz -36.806278 -18.292723 64.461525
On 06/05/2020 15:23, Bruce Fischl wrote:
hmm, that is not an icosahedral surface, which should have 160K vertices. Can you check your input surface? You'll also need to fix your freeview problem, but someone else will have to help you with that On Wed, 6 May 2020, Ian Hardingham wrote:
External Email - Use Caution
FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines?
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-0.9990, -0.0436, 0.0000) y_(ras) : (-0.0436, 0.9990, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.00000 92.25847; -0.04362 0.99905 0.00000 -99.12585; 0.00000 0.00000 1.00000 -145.07230; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 88.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 112.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talairach_flag 0 rescale 0.000000 nvertices 102020 nfaces 204036 total_area 65520.492188 group_avg_vtxarea_loaded 0 avgvtxarea 0.642232 avgvtxdist 0.940503 stdvtxdist 0.417776 vtx0xyz -8.576451 -101.319672 3.333434
On 06/05/2020 15:00, Bruce Fischl wrote: 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 Caution 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 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.freesur
fer.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:
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
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
sorry, I'm going to defer to Doug on surf2surf On Wed, 6 May 2020, Ian Hardingham wrote:
External Email - Use Caution
Thanks Bruce.
So a reminder I'm calling:
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
I'm assuming that means the "input surface" is /usr/local/freesurfer/subjects/fsaverage/surf/lh.white, and here's the mris_info for that, but bear in mind that I don't know for sure from that line that that's what is being used.
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 163842 num faces : 327680 num strips : 0 surface area: 65417 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 group avg surface area: 82220 ctr : (-31.9282, -18.8144, 16.3699) vertex locs : surfaceRAS talairch.xfm: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; surfaceRAS to talaraiched surfaceRAS: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; talairached surfaceRAS to surfaceRAS: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Volume Geometry (vg) volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 0.0000, 0.0000, 0.0000) file : ../mri/orig.mgz Volume Geometry vox2ras -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mris_info creationtime 2020/05/06-14:31:38-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /usr/local/freesurfer/subjects/fsaverage/surf/lh.white hemicode 0 talairach_flag 0 rescale 0.000000 nvertices 163842 nfaces 327680 total_area 65416.984375 group_avg_surf_area 82219.960938 group_avg_vtxarea_loaded 1 avgvtxarea 0.399269 avgvtxdist 0.721953 stdvtxdist 0.195470 vtx0xyz -36.806278 -18.292723 64.461525
On 06/05/2020 15:23, Bruce Fischl wrote: hmm, that is not an icosahedral surface, which should have 160K vertices. Can you check your input surface? You'll also need to fix your freeview problem, but someone else will have to help you with that On Wed, 6 May 2020, Ian Hardingham wrote:
External Email - Use Caution FSLInfo attached, thanks Bruce. When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines? SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-0.9990, -0.0436, 0.0000) y_(ras) : (-0.0436, 0.9990, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.00000 92.25847; -0.04362 0.99905 0.00000 -99.12585; 0.00000 0.00000 1.00000 -145.07230; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 88.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 112.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talairach_flag 0 rescale 0.000000 nvertices 102020 nfaces 204036 total_area 65520.492188 group_avg_vtxarea_loaded 0 avgvtxarea 0.642232 avgvtxdist 0.940503 stdvtxdist 0.417776 vtx0xyz -8.576451 -101.319672 3.333434 On 06/05/2020 15:00, Bruce Fischl wrote: 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 Caution 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 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.freesur
fer.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: 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 _______________________________________________ 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
That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject)
On 5/6/2020 10:21 AM, Ian Hardingham wrote:
External Email - Use Caution
FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines?
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-0.9990, -0.0436, 0.0000) y_(ras) : (-0.0436, 0.9990, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.00000 92.25847; -0.04362 0.99905 0.00000 -99.12585; 0.00000 0.00000 1.00000 -145.07230; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 88.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 112.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talairach_flag 0 rescale 0.000000 nvertices 102020 nfaces 204036 total_area 65520.492188 group_avg_vtxarea_loaded 0 avgvtxarea 0.642232 avgvtxdist 0.940503 stdvtxdist 0.417776 vtx0xyz -8.576451 -101.319672 3.333434
On 06/05/2020 15:00, Bruce Fischl wrote:
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 Caution 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 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.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 > > _______________________________________________ > 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
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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Ok, thanks Doug, but I'm looking to get the positions of the source vertexes on the target brain, not the target subject's vertices...
On 06/05/2020 23:07, Douglas N. Greve wrote:
That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject)
On 5/6/2020 10:21 AM, Ian Hardingham wrote:
External Email - Use Caution
FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines?
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-0.9990, -0.0436, 0.0000) y_(ras) : (-0.0436, 0.9990, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.00000 92.25847; -0.04362 0.99905 0.00000 -99.12585; 0.00000 0.00000 1.00000 -145.07230; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 88.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 112.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talairach_flag 0 rescale 0.000000 nvertices 102020 nfaces 204036 total_area 65520.492188 group_avg_vtxarea_loaded 0 avgvtxarea 0.642232 avgvtxdist 0.940503 stdvtxdist 0.417776 vtx0xyz -8.576451 -101.319672 3.333434
On 06/05/2020 15:00, Bruce Fischl wrote:
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 Caution 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 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.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 >> >> _______________________________________________ >> 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
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
I don't understand. What is the difference between the target brain and the target subject's vertices?
On 5/7/2020 2:17 AM, Ian Hardingham wrote:
External Email - Use Caution
Ok, thanks Doug, but I'm looking to get the positions of the source vertexes on the target brain, not the target subject's vertices...
On 06/05/2020 23:07, Douglas N. Greve wrote:
That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject)
On 5/6/2020 10:21 AM, Ian Hardingham wrote:
External Email - Use Caution
FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines?
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-0.9990, -0.0436, 0.0000) y_(ras) : (-0.0436, 0.9990, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.00000 92.25847; -0.04362 0.99905 0.00000 -99.12585; 0.00000 0.00000 1.00000 -145.07230; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 88.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 112.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talairach_flag 0 rescale 0.000000 nvertices 102020 nfaces 204036 total_area 65520.492188 group_avg_vtxarea_loaded 0 avgvtxarea 0.642232 avgvtxdist 0.940503 stdvtxdist 0.417776 vtx0xyz -8.576451 -101.319672 3.333434
On 06/05/2020 15:00, Bruce Fischl wrote:
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 Caution 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 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.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 >>> >>> _______________________________________________ >>> 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
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
External Email - Use Caution
I'd like to get a set of points to compare across several brains, so that the nth point in brain A is in roughly the same place as the nth point in brain B - so I'd like to have an agreed upon set of vertices (the source brain's vertices) translated to positions on the target brain (which may well not be vertices in the target geometry.)
On 07/05/2020 15:59, Douglas N. Greve wrote:
I don't understand. What is the difference between the target brain and the target subject's vertices?
On 5/7/2020 2:17 AM, Ian Hardingham wrote:
External Email - Use Caution
Ok, thanks Doug, but I'm looking to get the positions of the source vertexes on the target brain, not the target subject's vertices...
On 06/05/2020 23:07, Douglas N. Greve wrote:
That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject)
On 5/6/2020 10:21 AM, Ian Hardingham wrote:
External Email - Use Caution
FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines?
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-0.9990, -0.0436, 0.0000) y_(ras) : (-0.0436, 0.9990, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.00000 92.25847; -0.04362 0.99905 0.00000 -99.12585; 0.00000 0.00000 1.00000 -145.07230; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 88.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 112.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talairach_flag 0 rescale 0.000000 nvertices 102020 nfaces 204036 total_area 65520.492188 group_avg_vtxarea_loaded 0 avgvtxarea 0.642232 avgvtxdist 0.940503 stdvtxdist 0.417776 vtx0xyz -8.576451 -101.319672 3.333434
On 06/05/2020 15:00, Bruce Fischl wrote:
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 Caution 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 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.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 >>>> >>>> _______________________________________________ >>>> 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
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It comes down to how you want to define "roughly in the same place". Does this mean an affine (12dof) transform? And what information do you want? An XYZ coordinate?
On 5/7/2020 11:06 AM, Ian Hardingham wrote:
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I'd like to get a set of points to compare across several brains, so that the nth point in brain A is in roughly the same place as the nth point in brain B - so I'd like to have an agreed upon set of vertices (the source brain's vertices) translated to positions on the target brain (which may well not be vertices in the target geometry.)
On 07/05/2020 15:59, Douglas N. Greve wrote:
I don't understand. What is the difference between the target brain and the target subject's vertices?
On 5/7/2020 2:17 AM, Ian Hardingham wrote:
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Ok, thanks Doug, but I'm looking to get the positions of the source vertexes on the target brain, not the target subject's vertices...
On 06/05/2020 23:07, Douglas N. Greve wrote:
That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject)
On 5/6/2020 10:21 AM, Ian Hardingham wrote:
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FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines?
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-0.9990, -0.0436, 0.0000) y_(ras) : (-0.0436, 0.9990, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.00000 92.25847; -0.04362 0.99905 0.00000 -99.12585; 0.00000 0.00000 1.00000 -145.07230; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 88.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 112.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talairach_flag 0 rescale 0.000000 nvertices 102020 nfaces 204036 total_area 65520.492188 group_avg_vtxarea_loaded 0 avgvtxarea 0.642232 avgvtxdist 0.940503 stdvtxdist 0.417776 vtx0xyz -8.576451 -101.319672 3.333434
On 06/05/2020 15:00, Bruce Fischl wrote:
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 Caution > 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 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.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 >>>>> >>>>> _______________________________________________ >>>>> 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 >
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Thanks Doug - yes, I'd like the vertex coordinates in the same format as the local subject surface files are in.
On 07/05/2020 19:02, Douglas N. Greve wrote:
It comes down to how you want to define "roughly in the same place". Does this mean an affine (12dof) transform? And what information do you want? An XYZ coordinate?
On 5/7/2020 11:06 AM, Ian Hardingham wrote:
External Email - Use Caution
I'd like to get a set of points to compare across several brains, so that the nth point in brain A is in roughly the same place as the nth point in brain B - so I'd like to have an agreed upon set of vertices (the source brain's vertices) translated to positions on the target brain (which may well not be vertices in the target geometry.)
On 07/05/2020 15:59, Douglas N. Greve wrote:
I don't understand. What is the difference between the target brain and the target subject's vertices?
On 5/7/2020 2:17 AM, Ian Hardingham wrote:
External Email - Use Caution
Ok, thanks Doug, but I'm looking to get the positions of the source vertexes on the target brain, not the target subject's vertices...
On 06/05/2020 23:07, Douglas N. Greve wrote:
That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject)
On 5/6/2020 10:21 AM, Ian Hardingham wrote:
External Email - Use Caution
FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines?
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-0.9990, -0.0436, 0.0000) y_(ras) : (-0.0436, 0.9990, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.00000 92.25847; -0.04362 0.99905 0.00000 -99.12585; 0.00000 0.00000 1.00000 -145.07230; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 88.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 112.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talairach_flag 0 rescale 0.000000 nvertices 102020 nfaces 204036 total_area 65520.492188 group_avg_vtxarea_loaded 0 avgvtxarea 0.642232 avgvtxdist 0.940503 stdvtxdist 0.417776 vtx0xyz -8.576451 -101.319672 3.333434
On 06/05/2020 15:00, Bruce Fischl wrote: > 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 Caution >> 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 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.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 >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >> > > _______________________________________________ > 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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Isn't that what you got from the mri_surf2surf command?
On 5/7/2020 3:08 PM, Ian Hardingham wrote:
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Thanks Doug - yes, I'd like the vertex coordinates in the same format as the local subject surface files are in.
On 07/05/2020 19:02, Douglas N. Greve wrote:
It comes down to how you want to define "roughly in the same place". Does this mean an affine (12dof) transform? And what information do you want? An XYZ coordinate?
On 5/7/2020 11:06 AM, Ian Hardingham wrote:
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I'd like to get a set of points to compare across several brains, so that the nth point in brain A is in roughly the same place as the nth point in brain B - so I'd like to have an agreed upon set of vertices (the source brain's vertices) translated to positions on the target brain (which may well not be vertices in the target geometry.)
On 07/05/2020 15:59, Douglas N. Greve wrote:
I don't understand. What is the difference between the target brain and the target subject's vertices?
On 5/7/2020 2:17 AM, Ian Hardingham wrote:
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Ok, thanks Doug, but I'm looking to get the positions of the source vertexes on the target brain, not the target subject's vertices...
On 06/05/2020 23:07, Douglas N. Greve wrote:
That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject)
On 5/6/2020 10:21 AM, Ian Hardingham wrote: > > External Email - Use Caution > > FSLInfo attached, thanks Bruce. > > When trying to run freeview I get "freeview.bin: error while > loading shared libraries: libpng12.so.0: cannot open shared > object file: No such file or directory" - do I need to add > /usr/local/freesurfer/lib/* to path or something along those lines? > > SURFACE INFO ======================================== > type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE > num vertices: 102020 > num faces : 204036 > num strips : 0 > surface area: 65520.5 > AvgVtxArea 0.642232 > AvgVtxDist 0.940503 > StdVtxDist 0.417776 > ctr : (-31.9056, -18.8197, 16.3545) > vertex locs : surfaceRAS > Volume Geometry (vg) > volume geometry: > extent : (176, 224, 256) > voxel : ( 1.0000, 1.0000, 1.0000) > x_(ras) : (-0.9990, -0.0436, 0.0000) > y_(ras) : (-0.0436, 0.9990, 0.0000) > z_(ras) : ( 0.0000, 0.0000, 1.0000) > c_(ras) : (-0.5431, 8.9290, -17.0723) > file : /media/ian/bronson/subject/T1_nifti.nii.gz > Volume Geometry vox2ras > -0.99905 -0.04362 0.00000 92.25847; > -0.04362 0.99905 0.00000 -99.12585; > 0.00000 0.00000 1.00000 -145.07230; > 0.00000 0.00000 0.00000 1.00000; > Volume Geometry vox2ras-tkr > -1.00000 0.00000 0.00000 88.00000; > 0.00000 0.00000 1.00000 -128.00000; > 0.00000 -1.00000 0.00000 112.00000; > 0.00000 0.00000 0.00000 1.00000; > cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig > ProgramVersion: $Name: stable5 $ TimeStamp: > 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 > CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 > nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox > Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: > GCC CompilerVersion: 30400 > cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 > brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: > stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: > May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 > 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: > xubuntu-VirtualBox Platform: Linux PlatformVersion: > 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 > cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white > ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: > 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 > CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ > User: fsuser Machine: xubuntu-VirtualBox Platform: Linux > PlatformVersion: 3.2.0-23-generic CompilerName: GCC > CompilerVersion: 30400 > cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated > ProgramVersion: $Name: stable5 $ TimeStamp: > 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 > CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ > User: fsuser Machine: xubuntu-VirtualBox Platform: Linux > PlatformVersion: 3.2.0-23-generic CompilerName: GCC > CompilerVersion: 30400 > cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated > ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: > 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 > CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ > User: fsuser Machine: xubuntu-VirtualBox Platform: Linux > PlatformVersion: 3.2.0-23-generic CompilerName: GCC > CompilerVersion: 30400 > cmd[5]: mris_register -curv ../surf/lh.sphere > /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif > ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ > TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 > 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 > nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: > Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC > CompilerVersion: 30400 > mris_info > creationtime 2020/05/06-14:18:48-GMT > sysname Linux > hostname ryzen-cumnor > machine x86_64 > surfacefile /home/ian/cdm_registered_test/registered_lh.white > hemicode 1 > talairach_flag 0 > rescale 0.000000 > nvertices 102020 > nfaces 204036 > total_area 65520.492188 > group_avg_vtxarea_loaded 0 > avgvtxarea 0.642232 > avgvtxdist 0.940503 > stdvtxdist 0.417776 > vtx0xyz -8.576451 -101.319672 3.333434 > > On 06/05/2020 15:00, Bruce Fischl wrote: >> 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 Caution >>> 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 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.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 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>> >> >> _______________________________________________ >> 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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I don't see how it's possible I got a comparable list of points when the input was in the order of 300k verts, and the ouput was 180k verts - I would need the number of output verts to be exactly the same as the number of input verts.
On 07/05/2020 22:45, Douglas N. Greve wrote:
Isn't that what you got from the mri_surf2surf command?
On 5/7/2020 3:08 PM, Ian Hardingham wrote:
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Thanks Doug - yes, I'd like the vertex coordinates in the same format as the local subject surface files are in.
On 07/05/2020 19:02, Douglas N. Greve wrote:
It comes down to how you want to define "roughly in the same place". Does this mean an affine (12dof) transform? And what information do you want? An XYZ coordinate?
On 5/7/2020 11:06 AM, Ian Hardingham wrote:
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I'd like to get a set of points to compare across several brains, so that the nth point in brain A is in roughly the same place as the nth point in brain B - so I'd like to have an agreed upon set of vertices (the source brain's vertices) translated to positions on the target brain (which may well not be vertices in the target geometry.)
On 07/05/2020 15:59, Douglas N. Greve wrote:
I don't understand. What is the difference between the target brain and the target subject's vertices?
On 5/7/2020 2:17 AM, Ian Hardingham wrote:
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Ok, thanks Doug, but I'm looking to get the positions of the source vertexes on the target brain, not the target subject's vertices...
On 06/05/2020 23:07, Douglas N. Greve wrote: > That looks like it could be right. It has 102,020 vertices, > which should be the number of vertices in the target subject > (and is in the typical range for an individual subject) > > On 5/6/2020 10:21 AM, Ian Hardingham wrote: >> >> External Email - Use Caution >> >> FSLInfo attached, thanks Bruce. >> >> When trying to run freeview I get "freeview.bin: error while >> loading shared libraries: libpng12.so.0: cannot open shared >> object file: No such file or directory" - do I need to add >> /usr/local/freesurfer/lib/* to path or something along those lines? >> >> SURFACE INFO ======================================== >> type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE >> num vertices: 102020 >> num faces : 204036 >> num strips : 0 >> surface area: 65520.5 >> AvgVtxArea 0.642232 >> AvgVtxDist 0.940503 >> StdVtxDist 0.417776 >> ctr : (-31.9056, -18.8197, 16.3545) >> vertex locs : surfaceRAS >> Volume Geometry (vg) >> volume geometry: >> extent : (176, 224, 256) >> voxel : ( 1.0000, 1.0000, 1.0000) >> x_(ras) : (-0.9990, -0.0436, 0.0000) >> y_(ras) : (-0.0436, 0.9990, 0.0000) >> z_(ras) : ( 0.0000, 0.0000, 1.0000) >> c_(ras) : (-0.5431, 8.9290, -17.0723) >> file : /media/ian/bronson/subject/T1_nifti.nii.gz >> Volume Geometry vox2ras >> -0.99905 -0.04362 0.00000 92.25847; >> -0.04362 0.99905 0.00000 -99.12585; >> 0.00000 0.00000 1.00000 -145.07230; >> 0.00000 0.00000 0.00000 1.00000; >> Volume Geometry vox2ras-tkr >> -1.00000 0.00000 0.00000 88.00000; >> 0.00000 0.00000 1.00000 -128.00000; >> 0.00000 -1.00000 0.00000 112.00000; >> 0.00000 0.00000 0.00000 1.00000; >> cmd[0]: mris_remove_intersection ../surf/lh.orig >> ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: >> 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 >> CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 >> nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox >> Platform: Linux PlatformVersion: 3.2.0-23-generic >> CompilerName: GCC CompilerVersion: 30400 >> cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 >> brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: >> stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: >> May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v >> 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser >> Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: >> 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 >> cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white >> ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ >> TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 >> 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 >> nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox >> Platform: Linux PlatformVersion: 3.2.0-23-generic >> CompilerName: GCC CompilerVersion: 30400 >> cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated >> ProgramVersion: $Name: stable5 $ TimeStamp: >> 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 >> CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp >> $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux >> PlatformVersion: 3.2.0-23-generic CompilerName: GCC >> CompilerVersion: 30400 >> cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated >> ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: >> 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 >> CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ >> User: fsuser Machine: xubuntu-VirtualBox Platform: Linux >> PlatformVersion: 3.2.0-23-generic CompilerName: GCC >> CompilerVersion: 30400 >> cmd[5]: mris_register -curv ../surf/lh.sphere >> /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif >> ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ >> TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 >> 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 >> nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox >> Platform: Linux PlatformVersion: 3.2.0-23-generic >> CompilerName: GCC CompilerVersion: 30400 >> mris_info >> creationtime 2020/05/06-14:18:48-GMT >> sysname Linux >> hostname ryzen-cumnor >> machine x86_64 >> surfacefile /home/ian/cdm_registered_test/registered_lh.white >> hemicode 1 >> talairach_flag 0 >> rescale 0.000000 >> nvertices 102020 >> nfaces 204036 >> total_area 65520.492188 >> group_avg_vtxarea_loaded 0 >> avgvtxarea 0.642232 >> avgvtxdist 0.940503 >> stdvtxdist 0.417776 >> vtx0xyz -8.576451 -101.319672 3.333434 >> >> On 06/05/2020 15:00, Bruce Fischl wrote: >>> 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 Caution >>>> 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 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.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 >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>> >>> >>> _______________________________________________ >>> 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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I'm just going to try this again, but this time with a different command:
mris_apply_reg --src-xyz /usr/local/freesurfer/subjects/fsaverage/surf/lh.white --trg /home/ian/lh_reg.white --streg /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg /obd-fs/proc/my_subject/freesurfer/surf/lh.sphere.reg"
This gives me the same issue - fsaverage/surf/lh.white has 300k+ points in it, and the output of this command has fewer than half that.
I do not understand what kind of registration would reduce the number of points. What is the relationship between the first point in --src_xyz file and the first point in the output registered file? If I halved the number of points in the input, would I expect the output to be half the size? Or less?
I'm sure there's a simple explanation that I don't have my head around just yet - thank you for your patience.
Ian
On 07/05/2020 22:45, Douglas N. Greve wrote:
Isn't that what you got from the mri_surf2surf command?
On 5/7/2020 3:08 PM, Ian Hardingham wrote:
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The registration registers the meshes, but it does not alter the number of vertices in them. There is no 1-to-1 correspondence between the vertices of the 2 meshes.
May I ask why you need this? What do you want to achieve?
Tim
On May 11, 2020 at 2:11 PM Ian ian@mode7.games wrote:
External Email - Use CautionI'm just going to try this again, but this time with a different command:
mris_apply_reg --src-xyz /usr/local/freesurfer/subjects/fsaverage/surf/lh.white --trg /home/ian/lh_reg.white --streg /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg /obd-fs/proc/my_subject/freesurfer/surf/lh.sphere.reg"
This gives me the same issue - fsaverage/surf/lh.white has 300k+ points in it, and the output of this command has fewer than half that.
I do not understand what kind of registration would reduce the number of points. What is the relationship between the first point in --src_xyz file and the first point in the output registered file? If I halved the number of points in the input, would I expect the output to be half the size? Or less?
I'm sure there's a simple explanation that I don't have my head around just yet - thank you for your patience.
Ian
On 07/05/2020 22:45, Douglas N. Greve wrote:
Isn't that what you got from the mri_surf2surf command?
On 5/7/2020 3:08 PM, Ian Hardingham wrote:
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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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Thanks Tim.
I'd like a set of points on the surface to compare across subjects, where there are the same number of points for each subject and they're roughly in the same "physiological position" on each subject. So again, if on my atlas I have a point which is at the top of the ctx-rh-fusiform sulcus, I'd like that point to be registered to the top of the ctx-rh-fusiform sulcus in my subjects.
On 11/05/2020 13:49, Tim Schäfer wrote:
External Email - Use CautionThe registration registers the meshes, but it does not alter the number of vertices in them. There is no 1-to-1 correspondence between the vertices of the 2 meshes.
May I ask why you need this? What do you want to achieve?
Tim
On May 11, 2020 at 2:11 PM Ian ian@mode7.games wrote:
External Email - Use CautionI'm just going to try this again, but this time with a different command:
mris_apply_reg --src-xyz /usr/local/freesurfer/subjects/fsaverage/surf/lh.white --trg /home/ian/lh_reg.white --streg /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg /obd-fs/proc/my_subject/freesurfer/surf/lh.sphere.reg"
This gives me the same issue - fsaverage/surf/lh.white has 300k+ points in it, and the output of this command has fewer than half that.
I do not understand what kind of registration would reduce the number of points. What is the relationship between the first point in --src_xyz file and the first point in the output registered file? If I halved the number of points in the input, would I expect the output to be half the size? Or less?
I'm sure there's a simple explanation that I don't have my head around just yet - thank you for your patience.
Ian
On 07/05/2020 22:45, Douglas N. Greve wrote:
Isn't that what you got from the mri_surf2surf command?
On 5/7/2020 3:08 PM, Ian Hardingham wrote:
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
Ian, it seems like you want two different things. When you run mri_surf2surf, it gives you an output that has the same number of vertices as the target which would allow you to do the one-to-one comparison that you want to do. But at the same time, there seems to be a problem with having the same number of vertices. I'm still confused as to what you want to do. If you want to do a one-to-one comparison, then you've got to change the number of vertices, unless I'm missing something.
On 5/11/2020 9:38 AM, Ian wrote:
External Email - Use Caution
Thanks Tim.
I'd like a set of points on the surface to compare across subjects, where there are the same number of points for each subject and they're roughly in the same "physiological position" on each subject. So again, if on my atlas I have a point which is at the top of the ctx-rh-fusiform sulcus, I'd like that point to be registered to the top of the ctx-rh-fusiform sulcus in my subjects.
On 11/05/2020 13:49, Tim Schäfer wrote:
External Email - Use CautionThe registration registers the meshes, but it does not alter the number of vertices in them. There is no 1-to-1 correspondence between the vertices of the 2 meshes.
May I ask why you need this? What do you want to achieve?
Tim
On May 11, 2020 at 2:11 PM Ianian@mode7.games wrote:
External Email - Use CautionI'm just going to try this again, but this time with a different command:
mris_apply_reg --src-xyz /usr/local/freesurfer/subjects/fsaverage/surf/lh.white --trg /home/ian/lh_reg.white --streg /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg /obd-fs/proc/my_subject/freesurfer/surf/lh.sphere.reg"
This gives me the same issue - fsaverage/surf/lh.white has 300k+ points in it, and the output of this command has fewer than half that.
I do not understand what kind of registration would reduce the number of points. What is the relationship between the first point in --src_xyz file and the first point in the output registered file? If I halved the number of points in the input, would I expect the output to be half the size? Or less?
I'm sure there's a simple explanation that I don't have my head around just yet - thank you for your patience.
Ian
On 07/05/2020 22:45, Douglas N. Greve wrote:
Isn't that what you got from the mri_surf2surf command?
On 5/7/2020 3:08 PM, Ian Hardingham wrote:
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
--
*Ian Hardingham*
Chief Technology Officer
signature_873986710
ian.hardingham@oxfordbraindiagnostics.com mailto:terry.pollard@oxfordbraindiagnostics.com
+44 (0)7789 770555
Oxford Centre for Innovation | New Road | Oxford | OX1 1BY
Oxford Brain Diagnostics Ltd is a company registered in England and Wales | Company No. 11703979 | VAT No. 321 3026 62
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks for the reply Doug.
I'm looking for the same number of verts as the *subject* - maybe it's as simple as I should be registering the subjects *to* the FS average subject? But the problem is that I want the points in subject space, not average space.
So if I have five subjects - I would like the same number of points for each one, which I thought I would get by registering the average to each of them...
On 11/05/2020 18:56, Douglas N. Greve wrote:
Ian, it seems like you want two different things. When you run mri_surf2surf, it gives you an output that has the same number of vertices as the target which would allow you to do the one-to-one comparison that you want to do. But at the same time, there seems to be a problem with having the same number of vertices. I'm still confused as to what you want to do. If you want to do a one-to-one comparison, then you've got to change the number of vertices, unless I'm missing something.
On 5/11/2020 9:38 AM, Ian wrote:
External Email - Use Caution
Thanks Tim.
I'd like a set of points on the surface to compare across subjects, where there are the same number of points for each subject and they're roughly in the same "physiological position" on each subject. So again, if on my atlas I have a point which is at the top of the ctx-rh-fusiform sulcus, I'd like that point to be registered to the top of the ctx-rh-fusiform sulcus in my subjects.
On 11/05/2020 13:49, Tim Schäfer wrote:
External Email - Use CautionThe registration registers the meshes, but it does not alter the number of vertices in them. There is no 1-to-1 correspondence between the vertices of the 2 meshes.
May I ask why you need this? What do you want to achieve?
Tim
On May 11, 2020 at 2:11 PM Ianian@mode7.games wrote:
External Email - Use CautionI'm just going to try this again, but this time with a different command:
mris_apply_reg --src-xyz /usr/local/freesurfer/subjects/fsaverage/surf/lh.white --trg /home/ian/lh_reg.white --streg /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg /obd-fs/proc/my_subject/freesurfer/surf/lh.sphere.reg"
This gives me the same issue - fsaverage/surf/lh.white has 300k+ points in it, and the output of this command has fewer than half that.
I do not understand what kind of registration would reduce the number of points. What is the relationship between the first point in --src_xyz file and the first point in the output registered file? If I halved the number of points in the input, would I expect the output to be half the size? Or less?
I'm sure there's a simple explanation that I don't have my head around just yet - thank you for your patience.
Ian
On 07/05/2020 22:45, Douglas N. Greve wrote:
Isn't that what you got from the mri_surf2surf command?
On 5/7/2020 3:08 PM, Ian Hardingham wrote:
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
--
*Ian Hardingham*
Chief Technology Officer
signature_873986710
ian.hardingham@oxfordbraindiagnostics.com mailto:terry.pollard@oxfordbraindiagnostics.com
+44 (0)7789 770555
Oxford Centre for Innovation | New Road | Oxford | OX1 1BY
Oxford Brain Diagnostics Ltd is a company registered in England and Wales | Company No. 11703979 | VAT No. 321 3026 62
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@nmr.mgh.harvard.edu
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