Hi Doug, Thanks for your reply. I have downloaded some freesurfer files (.annot, .label, .curv, .w) about the specific regions. And I want to convert this files to volumetric masks, then the masks are used to overlay the normalized functional data, and according to the mask to define the specific region as roi. Thus, the problem is that, how I can achieve this goal, and which commands should I use. Thanks a lot. Best wishes, Meng
Date: Mon, 29 Apr 2013 17:30:14 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] convert labels to volumetric masks To: freesurfer@nmr.mgh.harvard.edu Message-ID: 517EE666.8050301@nmr.mgh.harvard.edu Content-Type: text/plain; charset=UTF-8; format=flowed
Hi Meng, I don't understand what you are trying to do. Can you elaborate? That command will simply check a registration that already exists. doug On 04/29/2013 10:36 AM, limengsecret wrote: Dear FreeSurfers, I want to convert cortical labels to volumetric masks, the mask created are used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. And if the command is wrong, which command should I use? Best wishes, Meng
Hi Meng,
On 04/30/2013 09:53 PM, limengsecret wrote:
Hi Doug, Thanks for your reply. I have downloaded some freesurfer files (.annot, .label, .curv, .w) about the specific regions.
what do you mean you downloaded them? where did they come from exactly? Are they your own data?
And I want to convert this files to volumetric masks, then the masks are used to overlay the normalized functional data, and according to the mask to define the specific region as roi.
How was your functional data normalized? Specifically what atlas was used?
Thus, the problem is that, how I can achieve this goal, and which commands should I use. Thanks a lot. Best wishes, Meng Date: Mon, 29 Apr 2013 17:30:14 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] convert labels to volumetric masks To: freesurfer@nmr.mgh.harvard.edu Message-ID: 517EE666.8050301@nmr.mgh.harvard.edu Content-Type: text/plain; charset=UTF-8; format=flowed Hi Meng, I don't understand what you are trying to do. Can you elaborate? That command will simply check a registration that already exists. doug On 04/29/2013 10:36 AM, limengsecret wrote: Dear FreeSurfers, I want to convert cortical labels to volumetric masks, the mask created are used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. And if the command is wrong, which command should I use? Best wishes, Meng
Hi Doug, The relative freesurfer files were downloaded from http://ltl.tkk.fi/wiki/Atlas about the retinotopic visual areas. And I want to convert the files to volumetric masks to use for my own data. The functional data have been preprocessed with slice-timing, realignment, and normalization. And the masks overlay the functional data created above to define the retinotopic visual areas. Thank you! Meng
发件人： Douglas N Greve 发送时间： 2013-05-02 02:02 收件人： limengsecret 抄送： freesurfer 主题： Re: [Freesurfer] convert labels to volumetric masks Hi Meng,
On 04/30/2013 09:53 PM, limengsecret wrote:
Hi Doug, Thanks for your reply. I have downloaded some freesurfer files (.annot, .label, .curv, .w) about the specific regions.
what do you mean you downloaded them? where did they come from exactly? Are they your own data?
And I want to convert this files to volumetric masks, then the masks are used to overlay the normalized functional data, and according to the mask to define the specific region as roi.
How was your functional data normalized? Specifically what atlas was used?
Thus, the problem is that, how I can achieve this goal, and which commands should I use. Thanks a lot. Best wishes, Meng Date: Mon, 29 Apr 2013 17:30:14 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] convert labels to volumetric masks To: freesurfer@nmr.mgh.harvard.edu Message-ID: 517EE666.8050301@nmr.mgh.harvard.edu Content-Type: text/plain; charset=UTF-8; format=flowed Hi Meng, I don't understand what you are trying to do. Can you elaborate? That command will simply check a registration that already exists. doug On 04/29/2013 10:36 AM, limengsecret wrote: Dear FreeSurfers, I want to convert cortical labels to volumetric masks, the mask created are used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. And if the command is wrong, which command should I use? Best wishes, Meng
Hi Meng, I don't know anything about that atlas. What space is it in? And how did you process the functional data?
On 5/1/13 9:14 PM, limengsecret wrote:
Hi Doug,
The relative freesurfer files were downloaded from http://ltl.tkk.fi/wiki/Atlas about the retinotopic visual areas. And I want to convert the files to volumetric masks to use for my own data.
The functional data have been preprocessed with slice-timing, realignment, and normalization. And the masks overlay the functional data created above to define the retinotopic visual areas.
Thank you!
Meng *发件人：* Douglas N Greve mailto:greve@nmr.mgh.harvard.edu *发送时间：* 2013-05-02 02:02 *收件人：* limengsecret mailto:limengsecret@126.com *抄送：* freesurfer mailto:freesurfer@nmr.mgh.harvard.edu *主题：* Re: [Freesurfer] convert labels to volumetric masks Hi Meng, On 04/30/2013 09:53 PM, limengsecret wrote:
Hi Doug, Thanks for your reply. I have downloaded some freesurfer files (.annot, .label, .curv, .w) about the specific regions.
what do you mean you downloaded them? where did they come from exactly? Are they your own data?
And I want to convert this files to volumetric masks, then the masks are used to overlay the normalized functional data, and according to the mask to define the specific region as roi.
How was your functional data normalized? Specifically what atlas was used?
Thus, the problem is that, how I can achieve this goal, and which commands should I use. Thanks a lot. Best wishes, Meng Date: Mon, 29 Apr 2013 17:30:14 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] convert labels to volumetric masks To: freesurfer@nmr.mgh.harvard.edu Message-ID: 517EE666.8050301@nmr.mgh.harvard.edu Content-Type: text/plain; charset=UTF-8; format=flowed Hi Meng, I don't understand what you are trying to do. Can you elaborate? That command will simply check a registration that already exists. doug On 04/29/2013 10:36 AM, limengsecret wrote: Dear FreeSurfers, I want to convert cortical labels to volumetric masks, the mask created are used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. And if the command is wrong, which command should I use? Best wishes, Meng
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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