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
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
External Email - Use Caution
Hi 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 CautionDear 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
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 Caution
Hi 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
you can use mri_segstats with the --slabel option
On 3/5/19 10:35 AM, Bruce Fischl wrote:
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 Caution
Hi 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@nmr.mgh.harvard.edu
-
310913949 -
Bruce Fischl -
Greve, Douglas N.,Ph.D.