Re: [Freesurfer] mri_extract issue

Hi Jie

Try using mri_extract.

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Jie Zhao Sent: Saturday, September 26, 2020 9:48 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_extract issue

External Email - Use Caution

Hi, Bruce

Yes, the head was cropped.How can I adjust the FOV?

My command line is: mri_convert -i orig.mgz -o origfinal.mgz --crop 160 160 160 --conform –nc

Thanks!

Jie

-----原始邮件----- 发件人:"Fischl, Bruce" <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> 发送时间:2020-09-26 23:31:33 (星期六) 收件人: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> 抄送: 主题: Re: [Freesurfer] mri_extract issue Hi Jie

Can you clarify what you mean by “head info. Disappeared in a sagittal slice”? Do you mean the head was cropped? If so, that probably just means you have to adjust the fov that you are cropping if you can.

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Jie Zhao Sent: Saturday, September 26, 2020 7:26 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_extract issue

External Email - Use Caution

Hi, Freesurfer Team

My input volume dimension is 248*176*320, so I use mri_extract scale to 256*256*256. However, the output volume lose some info. eg.some head info. disappeared in sagiital slice. How can scale my input voluem to 256*256*256, and also do not lose info.Thanks in advance!

All best,

Jie