External Email - Use Caution
Hi Bruce， The ‘mris_anatomical_stats‘’ and 'mri_segstats’ command line just output mean thickness of ROI, but I want to know cortical thickness for each vertex in the ROI. So I think the key is to find the coordination of each vertex in the ROI,but I dont know how. I found that the RAS coordinates in the lh.cortex.label do not correspond to the coordinates in the lh.thickness.
------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; 发送时间: 2019年3月5日(星期二) 晚上11:35 收件人: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu;
主题: Re: [Freesurfer] How to extract cortical features of a ROI
Hi Kan
you can give the surface-based label to mris_anatomical_stats and it will constrain it's calculations to the label (where it makes sense):
mris_anatomical_stats -l <path to your label> ...
you can probably do it with mri_segstats too - Doug will know
cheers Bruce
On Tue, 5 Mar 2019, 310913949 wrote:
External Email - Use CautionHi bruce?? I still have some questions about extracting cortical features of a ROI. I used the mri_label2label to sample the volumetric label to the surface of the subject. But I dont know how to do next, as i found that the RAS coordinates do not correspond to the coordinates in the lh.thickness, and why? Besides, I found the web of how to extract cortical thickness values for a region-of-interest (ROI) defined in volume space(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness).But it doesn't report the coordinates information. How can I get the ROI's coordinates information if i use this method? Thanks for your help! Kan Deng
------------------ Original ------------------ From: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; Date: Fri, Jan 25, 2019 10:58 PM To: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; Subject: Re: [Freesurfer] How to extract cortical features of a ROI
Hi Kan
if you draw a volumetric label you first need to sample it to the surface of that subject (mri_label2label --sample). If all you want are stats from the subject there is no need to map it to fsaverage - that is only necessary if you want to use a group coordinate system.
cheers Bruce
On Fri, 25 Jan 2019, 310913949 wrote:
External Email - Use Caution
Dear Freesurfer Experts, I want to extract cortical features of a ROI that I drawn manually on the rawavg.mgz in
Freesurfer, but i
don't know how to do that. I think maybe first the lesion mask should be registered to the
standard templates
fsaverage, but I don't know what the command line is , could you tell me? And secondly, I should
use
mri_label2label to map the label to individual subject and extract the cortical features of the
ROI, am I right?
I am looking forward to your reply!Thanks. Best wishes! Kan Deng
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
Oh, the vertex indices of the label are stored in the label file. You can use the. To index into the thickness vector Cheers Bruce
On Mar 5, 2019, at 10:09 PM, 310913949 310913949@qq.com wrote:
External Email - Use CautionHi Bruce， The ‘mris_anatomical_stats‘’ and 'mri_segstats’ command line just output mean thickness of ROI, but I want to know cortical thickness for each vertex in the ROI. So I think the key is to find the coordination of each vertex in the ROI,but I dont know how. I found that the RAS coordinates in the lh.cortex.label do not correspond to the coordinates in the lh.thickness.
------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; 发送时间: 2019年3月5日(星期二) 晚上11:35 收件人: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; 主题: Re: [Freesurfer] How to extract cortical features of a ROI
Hi Kan
you can give the surface-based label to mris_anatomical_stats and it will constrain it's calculations to the label (where it makes sense):
mris_anatomical_stats -l <path to your label> ...
you can probably do it with mri_segstats too - Doug will know
cheers Bruce
On Tue, 5 Mar 2019, 310913949 wrote:
External Email - Use CautionHi bruce?? I still have some questions about extracting cortical features of a ROI. I used the mri_label2label to sample the volumetric label to the surface of the subject. But I dont know how to do next, as i found that the RAS coordinates do not correspond to the coordinates in the lh.thickness, and why? Besides, I found the web of how to extract cortical thickness values for a region-of-interest (ROI) defined in volume space(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness).But it doesn't report the coordinates information. How can I get the ROI's coordinates information if i use this method? Thanks for your help! Kan Deng
------------------ Original ------------------ From: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; Date: Fri, Jan 25, 2019 10:58 PM To: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; Subject: Re: [Freesurfer] How to extract cortical features of a ROI
Hi Kan
if you draw a volumetric label you first need to sample it to the surface of that subject (mri_label2label --sample). If all you want are stats from the subject there is no need to map it to fsaverage - that is only necessary if you want to use a group coordinate system.
cheers Bruce
On Fri, 25 Jan 2019, 310913949 wrote:
External Email - Use Caution
Dear Freesurfer Experts, I want to extract cortical features of a ROI that I drawn manually on the rawavg.mgz in
Freesurfer, but i
don't know how to do that. I think maybe first the lesion mask should be registered to the
standard templates
fsaverage, but I don't know what the command line is , could you tell me? And secondly, I should
use
mri_label2label to map the label to individual subject and extract the cortical features of the
ROI, am I right?
I am looking forward to your reply!Thanks. Best wishes! Kan Deng
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@nmr.mgh.harvard.edu
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Bruce Fischl