Try it without the --sval (it will get the sval from the xyz in the surface).

doug

On Sun, 17 Feb 2008, Daniel Wakeman wrote:

Hi Doug,

Thanks.

I tried this and got the following:

[dw01@lws003 test2bem]$ mri_surf2surf --srcsubject $SUBJECT --sval-xyz smhead.surf --sval /imaging/dw01/simulation/subjects/p002/surf/ --trgsubject ico --trgicoorder 7 --tval /imaging/dw01/simulation/subjects/p002/surf/p002_outer_skin --tval-xyz --hemi lh Running mri_surf2surf on l25 surf2surf_nnfr(): Vals and Reg dimension mismatch nVals = 159416, nReg 153314 Segmentation fault Cut-and-paste the following info into your FreeSurfer problem report:

---

FREESURFER_HOME: /opt/freesurfer/

Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1

RedHat release: Red Hat Enterprise Linux WS release 4 (Nahant Update 5)

Kernel info: Linux 2.6.9-55.0.9.ELsmp i686

---

Please include the following additional information in your report:

1. subject name: p002
2. the entire command-line executed: above
3. the error message generated: above
4. optionally include the subject's /script/recon-all.log: NA

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

...

Try this instead:

mri_surf2surf --srcsubject $SUBJECT --sval-xyz $SUBJECTS_DIR/$SUBJECT/surf/lh.smseghead --trgsubject ico --tval $SUBJECTS_DIR/$SUBJECT/surf/$SUBJECT'_outer_skull' --tval-xyz --hemi lh

It is admittedly a little obtuse. mri_surf2surf was originally programmed to accept surface overlay and not surfaces themselves. --sval-xyz indicates that the input is a surface. --tval-xyz indicates that the output should be saved as a surface instead of an overlay.

doug

Daniel Wakeman wrote:

...

Hi,

I have a question (I believe about mri_surf2surf). First, I'll describe my goal:

I want to take a surface created with mri_tessellate and modified with mris_smooth and convert it to an isomorphic equally subdivided icosahedron (like mri_watershed creates).

e.g. take the lh.smseghead created by mkheadsurf and resample it:

mri_surf2surf --srcsubject $SUBJECT --srcsurfval $SUBJECTS_DIR/$SUBJECT/surf/lh.smseghead --src_type surf --trgsubject ico --trgsurfval $SUBJECTS_DIR/$SUBJECT/surf/$SUBJECT'_outer_skull' --hemi lh

I get the following error:

ERROR: could not determine type of /imaging/dw01/simulation/subjects/subject_02/surf/lh.smseghead

If this is possible, I want to know how I can correct my command.

Cheers, Dan

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Oh, I see the problem. It needs to have a registration surface to go from smhead to ico. You can't do what you want to do with mri_surf2surf (not sure what you can do).

doug

Daniel Wakeman wrote:

It still doesn't work. The error message is the same as the one I previously sent. Am I doing something wrong?

mri_surf2surf --srcsubject $SUBJECT --sval-xyz smhead.surf --trgsubject ico --trgicoorder 7 --tval /imaging/dw01/simulation/subjects/p002/surf/p002_outer_skin --tval-xyz --hemi lh

...

Try it without the --sval (it will get the sval from the xyz in the surface).

doug

On Sun, 17 Feb 2008, Daniel Wakeman wrote:

...

Hi Doug,

Thanks.

I tried this and got the following:

[dw01@lws003 test2bem]$ mri_surf2surf --srcsubject $SUBJECT --sval-xyz smhead.surf --sval /imaging/dw01/simulation/subjects/p002/surf/ --trgsubject ico --trgicoorder 7 --tval /imaging/dw01/simulation/subjects/p002/surf/p002_outer_skin --tval-xyz --hemi lh Running mri_surf2surf on l25 surf2surf_nnfr(): Vals and Reg dimension mismatch nVals = 159416, nReg 153314 Segmentation fault Cut-and-paste the following info into your FreeSurfer problem report:

---

FREESURFER_HOME: /opt/freesurfer/

Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1

RedHat release: Red Hat Enterprise Linux WS release 4 (Nahant Update 5)

Kernel info: Linux 2.6.9-55.0.9.ELsmp i686

---

Please include the following additional information in your report:

1. subject name: p002
2. the entire command-line executed: above
3. the error message generated: above
4. optionally include the subject's /script/recon-all.log: NA

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

...

Try this instead:

mri_surf2surf --srcsubject $SUBJECT --sval-xyz $SUBJECTS_DIR/$SUBJECT/surf/lh.smseghead --trgsubject ico --tval $SUBJECTS_DIR/$SUBJECT/surf/$SUBJECT'_outer_skull' --tval-xyz --hemi lh

It is admittedly a little obtuse. mri_surf2surf was originally programmed to accept surface overlay and not surfaces themselves. --sval-xyz indicates that the input is a surface. --tval-xyz indicates that the output should be saved as a surface instead of an overlay.

doug

Daniel Wakeman wrote:

...

Hi,

I have a question (I believe about mri_surf2surf). First, I'll describe my goal:

I want to take a surface created with mri_tessellate and modified with mris_smooth and convert it to an isomorphic equally subdivided icosahedron (like mri_watershed creates).

e.g. take the lh.smseghead created by mkheadsurf and resample it:

mri_surf2surf --srcsubject $SUBJECT --srcsurfval $SUBJECTS_DIR/$SUBJECT/surf/lh.smseghead --src_type surf --trgsubject ico --trgsurfval $SUBJECTS_DIR/$SUBJECT/surf/$SUBJECT'_outer_skull' --hemi lh

I get the following error:

ERROR: could not determine type of /imaging/dw01/simulation/subjects/subject_02/surf/lh.smseghead

If this is possible, I want to know how I can correct my command.

Cheers, Dan

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting