Hi Tina

can you send me the ascii file? Note that we assume in many places that the surface files start with a hemisphere specifier, so your output should probably be lh.neo024_2_pial or something like that. I doubt that's why it's crashing though Bruce On Fri, 17 May 2013, Tina Jeon wrote:

Dear Bruce,

Yes I have,

My input:

mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial Segmentation fault

Can you lead me as to why there is an error?

Thank you,

Tina

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 5:49 PM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] conversion from ascii to surface

Hi Tina

try mris_convert

cheers Bruce On Thu, 16 May 2013, Tina Jeon wrote:

...

Dear Doug, Nick, and all,

I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer.

Do you have any suggestions for how I could do the conversion?

Thank you in advance!

All the best

Tina Jeon

PhD Candidate

UT Southwestern Medical Center ‘14

---

---

UT Southwestern Medical Center The future of medicine, today.

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi Tina

how did you create the ascii file? The problem is that some of the faces contain vertex numbers that are you of range. Note that the vertex indices in the face list must be 0-based, not 1-based. Your file specifies 12722 vertices, but then lists some faces as having vertex number 12722 (which is out of bounds by 1).

cheers Bruce

On Fri, 17 May 2013, Tina Jeon wrote:

Here it is. I tried changing the name to lh.pial_neo024.asc but there was the same segmentation error.

Thank you Bruce, Cheers, Tina

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 8:57 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface

Hi Tina

can you send me the ascii file? Note that we assume in many places that the surface files start with a hemisphere specifier, so your output should probably be lh.neo024_2_pial or something like that. I doubt that's why it's crashing though Bruce On Fri, 17 May 2013, Tina Jeon wrote:

...

Dear Bruce,

Yes I have,

My input:

mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial Segmentation fault

Can you lead me as to why there is an error?

Thank you,

Tina

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 5:49 PM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] conversion from ascii to surface

Hi Tina

try mris_convert

cheers Bruce On Thu, 16 May 2013, Tina Jeon wrote:

...

Dear Doug, Nick, and all,

I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer.

Do you have any suggestions for how I could do the conversion?

Thank you in advance!

All the best

Tina Jeon

PhD Candidate

UT Southwestern Medical Center ‘14

---

_ ______

UT Southwestern Medical Center The future of medicine, today.

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

something is wrong as there should be no vertex indices > 12721

On Fri, 17 May 2013, Tina Jeon wrote:

I created the ascii file directly from amira, which from what I

understand is 0 based.

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 9:15 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface

Hi Tina

how did you create the ascii file? The problem is that some of the faces

contain vertex numbers that are you of range. Note that the vertex indices in the face list must be 0-based, not 1-based. Your file specifies 12722 vertices, but then lists some faces as having vertex number 12722 (which is out of bounds by 1). >

cheers Bruce

On Fri, 17 May 2013, Tina Jeon wrote:

...

Here it is. I tried changing the name to lh.pial_neo024.asc but there was the same segmentation error.

Thank you Bruce, Cheers, Tina

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 8:57 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface

Hi Tina

can you send me the ascii file? Note that we assume in many places that the surface files start with a hemisphere specifier, so your output should probably be lh.neo024_2_pial or something like that. I doubt that's why it's crashing though Bruce On Fri, 17 May 2013, Tina Jeon wrote:

...

Dear Bruce,

Yes I have,

My input:

mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial Segmentation fault

Can you lead me as to why there is an error?

Thank you,

Tina

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 5:49 PM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] conversion from ascii to surface

Hi Tina

try mris_convert

cheers Bruce On Thu, 16 May 2013, Tina Jeon wrote:

...

Dear Doug, Nick, and all,

I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer.

Do you have any suggestions for how I could do the conversion?

Thank you in advance!

All the best

Tina Jeon

PhD Candidate

UT Southwestern Medical Center ‘14

---

_ _ ______

UT Southwestern Medical Center The future of medicine, today.

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

sure. Glad it worked out Bruce On Fri, 17 May 2013, Tina Jeon wrote:

Great! I subtracted the vertices by one and now it works. Appreciate your help and fast responses.

Tina

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 9:37 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface

something is wrong as there should be no vertex indices > 12721

On Fri, 17 May 2013, Tina Jeon wrote:

...

I created the ascii file directly from amira, which from what I

understand is 0 based.

...

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 9:15 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface

Hi Tina

how did you create the ascii file? The problem is that some of the faces

contain vertex numbers that are you of range. Note that the vertex indices in the face list must be 0-based, not 1-based. Your file specifies 12722 vertices, but then lists some faces as having vertex number 12722 (which is out of bounds by 1). >

...

cheers Bruce

On Fri, 17 May 2013, Tina Jeon wrote:

...

Here it is. I tried changing the name to lh.pial_neo024.asc but there was the same segmentation error.

Thank you Bruce, Cheers, Tina

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 8:57 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface

Hi Tina

can you send me the ascii file? Note that we assume in many places that the surface files start with a hemisphere specifier, so your output should probably be lh.neo024_2_pial or something like that. I doubt that's why it's crashing though Bruce On Fri, 17 May 2013, Tina Jeon wrote:

...

Dear Bruce,

Yes I have,

My input:

mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial Segmentation fault

Can you lead me as to why there is an error?

Thank you,

Tina

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 5:49 PM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] conversion from ascii to surface

Hi Tina

try mris_convert

cheers Bruce On Thu, 16 May 2013, Tina Jeon wrote:

...

Dear Doug, Nick, and all,

I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer.

Do you have any suggestions for how I could do the conversion?

Thank you in advance!

All the best

Tina Jeon

PhD Candidate

UT Southwestern Medical Center ‘14

---

_ _ _ ______

UT Southwestern Medical Center The future of medicine, today.

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.