Re: [Freesurfer] Skin-Skull-Brain segmentation

[Douglas N. Greve]

You can try running samseg. This will generate most of the layers you 
want, but in segmentations. You will have to convert them to surfaces 
(eg, mri_tesssellate or mri_binarize with --surf output)


On 4/15/2024 5:31 AM, XIE Jing wrote:


External Email - Use Caution

Hello all,

We would like to use FreeSurfer to remodel the head, not only 
including the detailed brain structural information, but also 
considering skin and skull. I am wondering if the FreeSurfer is 
possible to split the skin, skull and brain surfaces at the same time?


We tried the syntax "mri_make_bem_surfaces -all" , and the error notes 
were received as follows:

/nvertices=2562, nfaces=5120 /
/mri_strip_skull: triangle file 
/home/customer/Desktop/headmodel/FREESURFER/freesurfer/lib/bem/ic4.tri 
read trishrink: File 
/home/customer/Desktop/headmodel/MRI/-all/mri/brain/COR-.info not found /

/Best guess at inner_skull.tri is in inner_skull_tmp.tri/

What's your suggestions and comments on this question? We appreciate 
it very much!


Thanks in advance!
Jing
*---*
*Jing XIE*
Associate Professor
Mechatronical Engineering
Beijing Institute of Technology
Beijing 180001, PR China


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[Freesurfer] Skin-Skull-Brain segmentation

[XIE Jing]

External Email - Use Caution

Hello all,

We would like to use FreeSurfer to remodel the head, not only including the 
detailed brain structural information, but also considering skin and skull. I 
am wondering if the FreeSurfer is possible to split the skin, skull and brain 
surfaces at the same time?

We tried the syntax "mri_make_bem_surfaces -all" , and the error notes were 
received as follows:
nvertices=2562, nfaces=5120
mri_strip_skull: triangle file 
/home/customer/Desktop/headmodel/FREESURFER/freesurfer/lib/bem/ic4.tri read 
trishrink: File /home/customer/Desktop/headmodel/MRI/-all/mri/brain/COR-.info 
not found
Best guess at inner_skull.tri is in inner_skull_tmp.tri

What's your suggestions and comments on this question? We appreciate it very 
much!

Thanks in advance!
Jing
---
Jing XIE
Associate Professor
Mechatronical Engineering
Beijing Institute of Technology
Beijing 180001, PR China

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.