Hello all,
I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsaverage template is not in the correct position. I’m guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance!
It is worth noting I am running Darwin-lion-stable-pub-v5.3.0
Best,
Michael S.
Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug
On 11/3/14 8:56 AM, Smith, Michael wrote:
Hello all,
I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I've noticed the ROI when registered to the fsaverage template is not in the correct position. I'm guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance!
It is worth noting I am running Darwin-lion-stable-pub-v5.3.0
Best,
Michael S.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
We are trying to look at the cortical thickness of a few different ROIs (primary auditory cortex) and see how these areas relate to the EEG ERPs we collected on these subjects as a function of age and development. I created the ROIs using the mri_annotation2label command per hemisphere then mri_label2vol to create a binary volume file for each ROI in each hemisphere. Does that sound correct or would you recommend doing it a different way?
Best,
Michael S.
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, November 3, 2014 at 9:31 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children
Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug
On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all,
I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsaverage template is not in the correct position. I’m guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance!
It is worth noting I am running Darwin-lion-stable-pub-v5.3.0
Best,
Michael S.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Did you make the from the ?h.aparc.annot of fsaverage? If so, why not make the label from the ?h.aparc.annot from the individual subject and then calculate the thickness from that? doug
On 11/3/14 9:44 AM, Smith, Michael wrote:
Hi Doug,
We are trying to look at the cortical thickness of a few different ROIs (primary auditory cortex) and see how these areas relate to the EEG ERPs we collected on these subjects as a function of age and development. I created the ROIs using the mri_annotation2label command per hemisphere then mri_label2vol to create a binary volume file for each ROI in each hemisphere. Does that sound correct or would you recommend doing it a different way?
Best,
Michael S.
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, November 3, 2014 at 9:31 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children
Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug
On 11/3/14 8:56 AM, Smith, Michael wrote:
Hello all,
I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I've noticed the ROI when registered to the fsaverage template is not in the correct position. I'm guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance!
It is worth noting I am running Darwin-lion-stable-pub-v5.3.0
Best,
Michael S.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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
I made the ROI on an individual subject basis, not from fsaverage. Not sure if the labels I made came from the .aparc.annot files, what is the default of mri_annotation2label? I used the -outdir flag.
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, November 3, 2014 at 10:10 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children
Did you make the from the ?h.aparc.annot of fsaverage? If so, why not make the label from the ?h.aparc.annot from the individual subject and then calculate the thickness from that? doug
On 11/3/14 9:44 AM, Smith, Michael wrote: Hi Doug,
We are trying to look at the cortical thickness of a few different ROIs (primary auditory cortex) and see how these areas relate to the EEG ERPs we collected on these subjects as a function of age and development. I created the ROIs using the mri_annotation2label command per hemisphere then mri_label2vol to create a binary volume file for each ROI in each hemisphere. Does that sound correct or would you recommend doing it a different way?
Best,
Michael S.
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, November 3, 2014 at 9:31 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children
Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug
On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all,
I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsaverage template is not in the correct position. I’m guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance!
It is worth noting I am running Darwin-lion-stable-pub-v5.3.0
Best,
Michael S.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Just wondering if you saw my response to your questions. Haven't heard anything from anyone else yet about my questions. Thanks in advance. In case you didn't see my response it is below:
I made the ROI on an individual subject basis, not from fsaverage. Not sure if the labels I made came from the .aparc.annot files, what is the default of mri_annotation2label? I used the -outdir flag.
Best,
Michael S.
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Monday, November 03, 2014 9:32 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children
Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all,
I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I've noticed the ROI when registered to the fsaverage template is not in the correct position. I'm guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance!
It is worth noting I am running Darwin-lion-stable-pub-v5.3.0
Best,
Michael S.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
In that case, can you just use the mean thickness values as listed in subject/stats/?h.aparc.stats ?
On 11/04/2014 10:33 AM, Smith, Michael wrote:
Hi Doug,
Just wondering if you saw my response to your questions. Haven’t heard anything from anyone else yet about my questions. Thanks in advance. In case you didn’t see my response it is below:
I made the ROI on an individual subject basis, not from fsaverage. Not sure if the labels I made came from the .aparc.annot files, what is the default of mri_annotation2label? I used the -outdir flag.
Best,
Michael S.
*From:*freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* Monday, November 03, 2014 9:32 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Fsaverage for ROI analysis of children
Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug
On 11/3/14 8:56 AM, Smith, Michael wrote:
Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsaverage template is not in the correct position. I’m guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance! It is worth noting I am running Darwin-lion-stable-pub-v5.3.0 Best, Michael S. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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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Douglas Greve -
Douglas N Greve
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Smith, Michael