Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation?
Any suggestions appreciated. Besh wishes.
Hi, In my case transformation to fsaverage did not work very well. What I did was: - from Surfrend page download Colin 27 subject and transform it to the latest version (now 5.2) - with bbregister obtain register.dat between this Colin 27 subject and SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good. - now you can import every AAL ROI (in .nii form) to an annotation or in the form of individual labels to your FS Colin 27, using the newly created registering file. - now you can use surf2surf or label2label to go to your subjects and obtain stats.
Br!
On 27/03/2013, at 05:35, ZhiLiangLong lagosslong1987@163.com wrote:
Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation?
Any suggestions appreciated. Besh wishes.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Dear Br: Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process. 1. You said I need transform the Colin 27 to the latest FS version (v.5.2). But i don't know how to do this. It is helpful if you can provide some information. 2. How does the Colin 27 space differs from fsaverage MNI305 space? The group analysis of cortical thickness is conducted in fsaverage space, after importing AAL ROI into Colin 27 space, should i transform the obtained ROI into fsaverage space? 3. i don't understand what is the register.dat between COlin 27 and SPM-s single subject t1.nii used for? I have tried the Surfrend, and found there was no entry for input of register file during the processing.
Looking forward to your reply. Best wishes.
zhiliang
At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi, In my case transformation to fsaverage did not work very well. What I did was: - from Surfrend page download Colin 27 subject and transform it to the latest version (now 5.2) - with bbregister obtain register.dat between this Colin 27 subject and SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good. - now you can import every AAL ROI (in .nii form) to an annotation or in the form of individual labels to your FS Colin 27, using the newly created registering file. - now you can use surf2surf or label2label to go to your subjects and obtain stats.
Br!
On 27/03/2013, at 05:35, ZhiLiangLong lagosslong1987@163.com wrote:
Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation?
Any suggestions appreciated. Besh wishes.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi Zhiliang, 1- well, I just recon-all-ed their subject again with the newest version. Recon-all -s Colin -all 2- maybe Doug or some other will answer this question better. I don't know the exact differences between fs mni305 and fs mnicolin27. What I know is that going the fsaverage path I couldn't obtain reliable transformations of the AAL labels. I think this was because fsaverage is very smoothed. Spm_register and vol2surf weren't working well.
The thing is, for group analysis, you can use Colin (or any other), as I understood it. When you use -qcache your data goes to fsaverage, but you can do it manually and specify that you want Colin instead (maybe someone can confirm it). If you are going to use just the AAL average CTs, then you just need to use surf2surf or label2label and you won't need fsaverage at all.
3- well, the spm single subject and Colin from Surfrend are the same subject but not exactly the same image. You do bbregister to them and obtain your register.dat matrix (you name it), and it goes from 2mm to 1mm and has some minimal translation. If you see both T1-s with tkregister you will see that they are almost the same (the spm version a little bit blurred, because of the resolution). You use this register.dat when doing vol2surf of the AAL.nii to your AAL.mgh surface ROI.
Hope this helps! Gari
On 27/03/2013, at 14:06, ZhiLiangLong lagosslong1987@163.com wrote:
Dear Br: Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process. 1. You said I need transform the Colin 27 to the latest FS version (v.5.2). But i don't know how to do this. It is helpful if you can provide some information.
2. How does the Colin 27 space differs from fsaverage MNI305 space? The group analysis of cortical thickness is conducted in fsaverage space, after importing AAL ROI into Colin 27 space, should i transform the obtained ROI into fsaverage space? 3. i don't understand what is the register.dat between COlin 27 and SPM-s single subject t1.nii used for? I have tried the Surfrend, and found there was no entry for input of register file during the processing.
Looking forward to your reply. Best wishes.
zhiliang
At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi, In my case transformation to fsaverage did not work very well. What I did was: - from Surfrend page download Colin 27 subject and transform it to the latest version (now 5.2) - with bbregister obtain register.dat between this Colin 27 subject and SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good. - now you can import every AAL ROI (in .nii form) to an annotation or in the form of individual labels to your FS Colin 27, using the newly created registering file. - now you can use surf2surf or label2label to go to your subjects and obtain stats.
Br!
On 27/03/2013, at 05:35, ZhiLiangLong lagosslong1987@163.com wrote:
Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation?
Any suggestions appreciated. Besh wishes.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Dear Gari: Thank you for give me suggestions patiently. i figured it out as you suggested. it works well. I have one more question: Do you know there are published papers which use the surface-based aal template (or something like this) to do research (e.g. cortical network analysis based on this template)?
Best wishes. zhiliang
At 2013-03-29 15:34:02,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi Zhiliang, 1- well, I just recon-all-ed their subject again with the newest version. Recon-all -s Colin -all 2- maybe Doug or some other will answer this question better. I don't know the exact differences between fs mni305 and fs mnicolin27. What I know is that going the fsaverage path I couldn't obtain reliable transformations of the AAL labels. I think this was because fsaverage is very smoothed. Spm_register and vol2surf weren't working well.
The thing is, for group analysis, you can use Colin (or any other), as I understood it. When you use -qcache your data goes to fsaverage, but you can do it manually and specify that you want Colin instead (maybe someone can confirm it). If you are going to use just the AAL average CTs, then you just need to use surf2surf or label2label and you won't need fsaverage at all.
3- well, the spm single subject and Colin from Surfrend are the same subject but not exactly the same image. You do bbregister to them and obtain your register.dat matrix (you name it), and it goes from 2mm to 1mm and has some minimal translation. If you see both T1-s with tkregister you will see that they are almost the same (the spm version a little bit blurred, because of the resolution). You use this register.dat when doing vol2surf of the AAL.nii to your AAL.mgh surface ROI.
Hope this helps! Gari
On 27/03/2013, at 14:06, ZhiLiangLong lagosslong1987@163.com wrote:
Dear Br: Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process. 1. You said I need transform the Colin 27 to the latest FS version (v.5.2). But i don't know how to do this. It is helpful if you can provide some information. 2. How does the Colin 27 space differs from fsaverage MNI305 space? The group analysis of cortical thickness is conducted in fsaverage space, after importing AAL ROI into Colin 27 space, should i transform the obtained ROI into fsaverage space? 3. i don't understand what is the register.dat between COlin 27 and SPM-s single subject t1.nii used for? I have tried the Surfrend, and found there was no entry for input of register file during the processing.
Looking forward to your reply. Best wishes.
zhiliang
At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi, In my case transformation to fsaverage did not work very well. What I did was: - from Surfrend page download Colin 27 subject and transform it to the latest version (now 5.2) - with bbregister obtain register.dat between this Colin 27 subject and SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good. - now you can import every AAL ROI (in .nii form) to an annotation or in the form of individual labels to your FS Colin 27, using the newly created registering file. - now you can use surf2surf or label2label to go to your subjects and obtain stats.
Br!
On 27/03/2013, at 05:35, ZhiLiangLong lagosslong1987@163.com wrote:
Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation?
Any suggestions appreciated. Besh wishes.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
I faced this problem a while ago. Both MNI to fsaverage, MNI itself and Colin27 didn't work sufficiently for sampling the labels, all had problems with the registration causing holes in the sulci and gyri ending up in the wrong label. (That might be 'good' since AAL is a volumetric atlas; but might also be bad, since you often don't want to look at an in complete label). I ended up making my own gcs fom a training set with mris_ca_train. Now I can segment surfaces just by calling mris_ca_label which works flawlessly and consistent throughout subjects.
Best,
Martijn
Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens ZhiLiangLong Verzonden: zaterdag 30 maart 2013 16:25 Aan: Garikoitz Lerma-Usabiaga CC: Freesurfer Onderwerp: Re: [Freesurfer] How to get surface-based AAL template
Dear Gari:
Thank you for give me suggestions patiently. i figured it out as you suggested. it works well. I have one more question: Do you know there are published papers which use the surface-based aal template (or something like this) to do research (e.g. cortical network analysis based on this template)?
Best wishes.
zhiliang
At 2013-03-29 15:34:02,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi Zhiliang,
1- well, I just recon-all-ed their subject again with the newest version. Recon-all -s Colin -all
2- maybe Doug or some other will answer this question better. I don't know the exact differences between fs mni305 and fs mnicolin27. What I know is that going the fsaverage path I couldn't obtain reliable transformations of the AAL labels. I think this was because fsaverage is very smoothed. Spm_register and vol2surf weren't working well.
The thing is, for group analysis, you can use Colin (or any other), as I understood it. When you use -qcache your data goes to fsaverage, but you can do it manually and specify that you want Colin instead (maybe someone can confirm it). If you are going to use just the AAL average CTs, then you just need to use surf2surf or label2label and you won't need fsaverage at all.
3- well, the spm single subject and Colin from Surfrend are the same subject but not exactly the same image. You do bbregister to them and obtain your register.dat matrix (you name it), and it goes from 2mm to 1mm and has some minimal translation. If you see both T1-s with tkregister you will see that they are almost the same (the spm version a little bit blurred, because of the resolution). You use this register.dat when doing vol2surf of the AAL.nii to your AAL.mgh surface ROI.
Hope this helps!
Gari
On 27/03/2013, at 14:06, ZhiLiangLong lagosslong1987@163.com wrote:
Dear Br:
Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process.
1. You said I need transform the Colin 27 to the latest FS version (v.5.2). But i don't know how to do this. It is helpful if you can provide some information.
2. How does the Colin 27 space differs from fsaverage MNI305 space? The group analysis of cortical thickness is conducted in fsaverage space, after importing AAL ROI into Colin 27 space, should i transform the obtained ROI into fsaverage space?
3. i don't understand what is the register.dat between COlin 27 and SPM-s single subject t1.nii used for? I have tried the Surfrend, and found there was no entry for input of register file during the processing.
Looking forward to your reply.
Best wishes.
zhiliang
At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi,
In my case transformation to fsaverage did not work very well. What I did was:
- from Surfrend page download Colin 27 subject and transform it to the latest version (now 5.2)
- with bbregister obtain register.dat between this Colin 27 subject and SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good.
- now you can import every AAL ROI (in .nii form) to an annotation or in the form of individual labels to your FS Colin 27, using the newly created registering file.
- now you can use surf2surf or label2label to go to your subjects and obtain stats.
Br!
On 27/03/2013, at 05:35, ZhiLiangLong lagosslong1987@163.com wrote:
Hi all;
I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation?
Any suggestions appreciated.
Besh wishes.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi Zhi Liang,
Out of curiosity, why not just use the FreeSurfer parcellations, so you don't end up with holes in the sulci/gyri?
--Thomas
On Sun, Mar 31, 2013 at 8:28 PM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote:
I faced this problem a while ago. Both MNI to fsaverage, MNI itself and Colin27 didn’t work sufficiently for sampling the labels, all had problems with the registration causing holes in the sulci and gyri ending up in the wrong label. (That might be ‘good’ since AAL is a volumetric atlas; but might also be bad, since you often don’t want to look at an in complete label). I ended up making my own gcs fom a training set with mris_ca_train. Now I can segment surfaces just by calling mris_ca_label which works flawlessly and consistent throughout subjects.
Best,
Martijn
Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens ZhiLiangLong Verzonden: zaterdag 30 maart 2013 16:25 Aan: Garikoitz Lerma-Usabiaga CC: Freesurfer Onderwerp: Re: [Freesurfer] How to get surface-based AAL template
Dear Gari:
Thank you for give me suggestions patiently. i figured it out as yousuggested. it works well. I have one more question: Do you know there are published papers which use the surface-based aal template (or something like this) to do research (e.g. cortical network analysis based on this template)?
Best wishes.
zhiliang
At 2013-03-29 15:34:02,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi Zhiliang,
1- well, I just recon-all-ed their subject again with the newest version. Recon-all -s Colin -all
2- maybe Doug or some other will answer this question better. I don't know the exact differences between fs mni305 and fs mnicolin27. What I know is that going the fsaverage path I couldn't obtain reliable transformations of the AAL labels. I think this was because fsaverage is very smoothed. Spm_register and vol2surf weren't working well.
The thing is, for group analysis, you can use Colin (or any other), as I understood it. When you use -qcache your data goes to fsaverage, but you can do it manually and specify that you want Colin instead (maybe someone can confirm it). If you are going to use just the AAL average CTs, then you just need to use surf2surf or label2label and you won't need fsaverage at all.
3- well, the spm single subject and Colin from Surfrend are the same subject but not exactly the same image. You do bbregister to them and obtain your register.dat matrix (you name it), and it goes from 2mm to 1mm and has some minimal translation. If you see both T1-s with tkregister you will see that they are almost the same (the spm version a little bit blurred, because of the resolution). You use this register.dat when doing vol2surf of the AAL.nii to your AAL.mgh surface ROI.
Hope this helps!
Gari
On 27/03/2013, at 14:06, ZhiLiangLong lagosslong1987@163.com wrote:
Dear Br:
Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process.
- You said I need transform the Colin 27 to the latest FS version
(v.5.2). But i don't know how to do this. It is helpful if you can provide some information.
- How does the Colin 27 space differs from fsaverage MNI305 space? The
group analysis of cortical thickness is conducted in fsaverage space, after importing AAL ROI into Colin 27 space, should i transform the obtained ROI into fsaverage space?
- i don't understand what is the register.dat between COlin 27 and SPM-s
single subject t1.nii used for? I have tried the Surfrend, and found there was no entry for input of register file during the processing.
Looking forward to your reply.
Best wishes.
zhiliang
At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi,
In my case transformation to fsaverage did not work very well. What I did was:
- from Surfrend page download Colin 27 subject and transform it to the
latest version (now 5.2)
- with bbregister obtain register.dat between this Colin 27 subject and
SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good.
- now you can import every AAL ROI (in .nii form) to an annotation or in the
form of individual labels to your FS Colin 27, using the newly created registering file.
- now you can use surf2surf or label2label to go to your subjects and obtain
stats.
Br!
On 27/03/2013, at 05:35, ZhiLiangLong lagosslong1987@163.com wrote:
Hi all;
I need a suface-based aal template which is compatible with FS surfacefile. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation?
Any suggestions appreciated.
Besh wishes.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi Thomas: There are no special reasons why i need the surface-based aal template. my goal is to parcellate surface into thousands of small brain areas, and construct large-scale cortical network. I have no idea how to segment the surface directly in FS. But i know the way to segment AAL template to the specific parcellation level (e.g. AAL-1024 ) i want. that is why i do this.
Best. zhiliang
At 2013-04-01 12:55:03,"Thomas Yeo" ythomas@csail.mit.edu wrote:
Hi Zhi Liang,
Out of curiosity, why not just use the FreeSurfer parcellations, so you don't end up with holes in the sulci/gyri?
--Thomas
On Sun, Mar 31, 2013 at 8:28 PM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote:
I faced this problem a while ago. Both MNI to fsaverage, MNI itself and Colin27 didn’t work sufficiently for sampling the labels, all had problems with the registration causing holes in the sulci and gyri ending up in the wrong label. (That might be ‘good’ since AAL is a volumetric atlas; but might also be bad, since you often don’t want to look at an in complete label). I ended up making my own gcs fom a training set with mris_ca_train. Now I can segment surfaces just by calling mris_ca_label which works flawlessly and consistent throughout subjects.
Best,
Martijn
Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens ZhiLiangLong
Verzonden: zaterdag 30 maart 2013 16:25 Aan: Garikoitz Lerma-Usabiaga CC: Freesurfer Onderwerp: Re: [Freesurfer] How to get surface-based AAL template
Dear Gari:
Thank you for give me suggestions patiently. i figured it out as yousuggested. it works well. I have one more question: Do you know there are published papers which use the surface-based aal template (or something like this) to do research (e.g. cortical network analysis based on this template)?
Best wishes.
zhiliang
At 2013-03-29 15:34:02,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi Zhiliang,
1- well, I just recon-all-ed their subject again with the newest version. Recon-all -s Colin -all
2- maybe Doug or some other will answer this question better. I don't know the exact differences between fs mni305 and fs mnicolin27. What I know is that going the fsaverage path I couldn't obtain reliable transformations of the AAL labels. I think this was because fsaverage is very smoothed. Spm_register and vol2surf weren't working well.
The thing is, for group analysis, you can use Colin (or any other), as I understood it. When you use -qcache your data goes to fsaverage, but you can do it manually and specify that you want Colin instead (maybe someone can confirm it). If you are going to use just the AAL average CTs, then you just need to use surf2surf or label2label and you won't need fsaverage at all.
3- well, the spm single subject and Colin from Surfrend are the same subject but not exactly the same image. You do bbregister to them and obtain your register.dat matrix (you name it), and it goes from 2mm to 1mm and has some minimal translation. If you see both T1-s with tkregister you will see that they are almost the same (the spm version a little bit blurred, because of the resolution). You use this register.dat when doing vol2surf of the AAL.nii to your AAL.mgh surface ROI.
Hope this helps!
Gari
On 27/03/2013, at 14:06, ZhiLiangLong lagosslong1987@163.com wrote:
Dear Br:
Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process.
- You said I need transform the Colin 27 to the latest FS version
(v.5.2). But i don't know how to do this. It is helpful if you can provide some information.
- How does the Colin 27 space differs from fsaverage MNI305 space? The
group analysis of cortical thickness is conducted in fsaverage space, after importing AAL ROI into Colin 27 space, should i transform the obtained ROI into fsaverage space?
- i don't understand what is the register.dat between COlin 27 and SPM-s
single subject t1.nii used for? I have tried the Surfrend, and found there was no entry for input of register file during the processing.
Looking forward to your reply.
Best wishes.
zhiliang
At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi,
In my case transformation to fsaverage did not work very well. What I did was:
- from Surfrend page download Colin 27 subject and transform it to the
latest version (now 5.2)
- with bbregister obtain register.dat between this Colin 27 subject and
SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good.
- now you can import every AAL ROI (in .nii form) to an annotation or in the
form of individual labels to your FS Colin 27, using the newly created registering file.
- now you can use surf2surf or label2label to go to your subjects and obtain
stats.
Br!
On 27/03/2013, at 05:35, ZhiLiangLong lagosslong1987@163.com wrote:
Hi all;
I need a suface-based aal template which is compatible with FS surfacefile. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation?
Any suggestions appreciated.
Besh wishes.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi Zhiliang
You can use
mris_make_face_parcellation
Or
mris_divide_parcellation
directly in FreeSurfer to produce your own parcellation scheme
Cheers Jürgen
On [DATE], "ZhiLiangLong" <[ADDRESS]> wrote:
Hi Thomas: There are no special reasons why i need the surface-based aal template. my goal is to parcellate surface into thousands of small brain areas, and construct large-scale cortical network. I have no idea how to segment the surface directly in FS. But i know the way to segment AAL template to the specific parcellation level (e.g. AAL-1024 ) i want. that is why i do this.
Best. zhiliang
At 2013-04-01 12:55:03,"Thomas Yeo" ythomas@csail.mit.edu wrote:
Hi Zhi Liang,
Out of curiosity, why not just use the FreeSurfer parcellations, so you don't end up with holes in the sulci/gyri?
--Thomas
On Sun, Mar 31, 2013 at 8:28 PM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote:
I faced this problem a while ago. Both MNI to fsaverage, MNI itself and Colin27 didn¹t work sufficiently for sampling the labels, all had
problems
with the registration causing holes in the sulci and gyri ending up in
the
wrong label. (That might be good¹ since AAL is a volumetric atlas; but might also be bad, since you often don¹t want to look at an in complete label). I ended up making my own gcs fom a training set with
mris_ca_train.
Now I can segment surfaces just by calling mris_ca_label which works flawlessly and consistent throughout subjects.
Best,
Martijn
Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens ZhiLiangLong
Verzonden: zaterdag 30 maart 2013 16:25 Aan: Garikoitz Lerma-Usabiaga CC: Freesurfer Onderwerp: Re: [Freesurfer] How to get surface-based AAL template
Dear Gari:
Thank you for give me suggestions patiently. i figured it out as yousuggested. it works well. I have one more question: Do you know there are published papers which use the surface-based aal template (or something
like
this) to do research (e.g. cortical network analysis based on this template)?
Best wishes.
zhiliang
At 2013-03-29 15:34:02,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi Zhiliang,
1- well, I just recon-all-ed their subject again with the newest version. Recon-all -s Colin -all
2- maybe Doug or some other will answer this question better. I don't >>>
know
the exact differences between fs mni305 and fs mnicolin27. What I know is that going the fsaverage path I couldn't obtain reliable transformations
of
the AAL labels. I think this was because fsaverage is very smoothed. Spm_register and vol2surf weren't working well.
The thing is, for group analysis, you can use Colin (or any other), as I understood it. When you use -qcache your data goes to fsaverage, but you
can
do it manually and specify that you want Colin instead (maybe someone can confirm it). If you are going to use just the AAL average CTs, then you
just
need to use surf2surf or label2label and you won't need fsaverage at all.
3- well, the spm single subject and Colin from Surfrend are the same
subject
but not exactly the same image. You do bbregister to them and obtain your register.dat matrix (you name it), and it goes from 2mm to 1mm and has
some
minimal translation. If you see both T1-s with tkregister you will see
that
they are almost the same (the spm version a little bit blurred, because
of
the resolution). You use this register.dat when doing vol2surf of the AAL.nii to your AAL.mgh surface ROI.
Hope this helps!
Gari
On 27/03/2013, at 14:06, ZhiLiangLong lagosslong1987@163.com wrote:
Dear Br:
Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process.
- You said I need transform the Colin 27 to the latest FS version
(v.5.2). But i don't know how to do this. It is helpful if you can
provide
some information.
- How does the Colin 27 space differs from fsaverage MNI305 space? The
group analysis of cortical thickness is conducted in fsaverage space,
after
importing AAL ROI into Colin 27 space, should i transform the obtained
ROI
into fsaverage space?
- i don't understand what is the register.dat between COlin 27 and
SPM-s
single subject t1.nii used for? I have tried the Surfrend, and found
there
was no entry for input of register file during the processing.
Looking forward to your reply.
Best wishes.
zhiliang
At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi,
In my case transformation to fsaverage did not work very well. What I did was:
- from Surfrend page download Colin 27 subject and transform it to the
latest version (now 5.2)
- with bbregister obtain register.dat between this Colin 27 subject and
SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s
are
defined in Colin 27. As they are the same subject, the registering is >>>
very
good.
- now you can import every AAL ROI (in .nii form) to an annotation or in
the
form of individual labels to your FS Colin 27, using the newly created registering file.
- now you can use surf2surf or label2label to go to your subjects and
obtain
stats.
Br!
On 27/03/2013, at 05:35, ZhiLiangLong lagosslong1987@163.com wrote:
Hi all;
I need a suface-based aal template which is compatible with FSsurface
file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct?
if
in this case, how can i do the transformation?
Any suggestions appreciated.
Besh wishes.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------
I believe that someone has created the AAL labels on the Colin 27 brain. These should be able to be transformed to the fsaverage brain.
I've contacted the person who said they had the files and will let you know if I get the files and am able to transform the files.
Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
On Mon, Apr 1, 2013 at 6:52 AM, Jürgen Hänggi j.haenggi@psychologie.uzh.chwrote:
Hi Zhiliang
You can use
mris_make_face_parcellation
Or
mris_divide_parcellation
directly in FreeSurfer to produce your own parcellation scheme
Cheers Jürgen
On [DATE], "ZhiLiangLong" <[ADDRESS]> wrote:
Hi Thomas: There are no special reasons why i need the surface-based aal template. my goal is to parcellate surface into thousands of small brain areas, and construct large-scale cortical network. I have no idea how to segment the surface directly in FS. But i know the way to segment AAL template to the specific parcellation level (e.g. AAL-1024 ) i want. that is why i do this.
Best. zhiliang
At 2013-04-01 12:55:03,"Thomas Yeo" ythomas@csail.mit.edu wrote:
Hi Zhi Liang,
Out of curiosity, why not just use the FreeSurfer parcellations, so you don't end up with holes in the sulci/gyri?
--Thomas
On Sun, Mar 31, 2013 at 8:28 PM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote:
I faced this problem a while ago. Both MNI to fsaverage, MNI itself and Colin27 didn’t work sufficiently for sampling the labels, all had
problems
with the registration causing holes in the sulci and gyri ending up in
the
wrong label. (That might be ‘good’ since AAL is a volumetric atlas; but might also be bad, since you often don’t want to look at an in complete label). I ended up making my own gcs fom a training set with
mris_ca_train.
Now I can segment surfaces just by calling mris_ca_label which works flawlessly and consistent throughout subjects.
Best,
Martijn
Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu]
Namens ZhiLiangLong
Verzonden: zaterdag 30 maart 2013 16:25 Aan: Garikoitz Lerma-Usabiaga CC: Freesurfer Onderwerp: Re: [Freesurfer] How to get surface-based AAL template
Dear Gari:
Thank you for give me suggestions patiently. i figured it out as yousuggested. it works well. I have one more question: Do you know there
are
published papers which use the surface-based aal template (or something
like
this) to do research (e.g. cortical network analysis based on this template)?
Best wishes.
zhiliang
At 2013-03-29 15:34:02,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi Zhiliang,
1- well, I just recon-all-ed their subject again with the newest
version.
Recon-all -s Colin -all
2- maybe Doug or some other will answer this question better. I don't
know
the exact differences between fs mni305 and fs mnicolin27. What I know
is
that going the fsaverage path I couldn't obtain reliable
transformations of
the AAL labels. I think this was because fsaverage is very smoothed. Spm_register and vol2surf weren't working well.
The thing is, for group analysis, you can use Colin (or any other), as I understood it. When you use -qcache your data goes to fsaverage, but
you can
do it manually and specify that you want Colin instead (maybe someone
can
confirm it). If you are going to use just the AAL average CTs, then you
just
need to use surf2surf or label2label and you won't need fsaverage at
all.
3- well, the spm single subject and Colin from Surfrend are the same
subject
but not exactly the same image. You do bbregister to them and obtain
your
register.dat matrix (you name it), and it goes from 2mm to 1mm and has
some
minimal translation. If you see both T1-s with tkregister you will see
that
they are almost the same (the spm version a little bit blurred, because
of
the resolution). You use this register.dat when doing vol2surf of the AAL.nii to your AAL.mgh surface ROI.
Hope this helps!
Gari
On 27/03/2013, at 14:06, ZhiLiangLong lagosslong1987@163.com wrote:
Dear Br:
Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process.
- You said I need transform the Colin 27 to the latest FS version
(v.5.2). But i don't know how to do this. It is helpful if you can
provide
some information.
- How does the Colin 27 space differs from fsaverage MNI305 space?
The
group analysis of cortical thickness is conducted in fsaverage space,
after
importing AAL ROI into Colin 27 space, should i transform the obtained
ROI
into fsaverage space?
- i don't understand what is the register.dat between COlin 27 and
SPM-s
single subject t1.nii used for? I have tried the Surfrend, and found
there
was no entry for input of register file during the processing.
Looking forward to your reply.
Best wishes.
zhiliang
At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" garikoitz@gmail.com wrote:
Hi,
In my case transformation to fsaverage did not work very well. What I
did
was:
- from Surfrend page download Colin 27 subject and transform it to the
latest version (now 5.2)
- with bbregister obtain register.dat between this Colin 27 subject and
SPM-s single subject t1.nii, which is the 2mm version of Colin 27.
AAL-s are
defined in Colin 27. As they are the same subject, the registering is
very
good.
- now you can import every AAL ROI (in .nii form) to an annotation or
in the
form of individual labels to your FS Colin 27, using the newly created registering file.
- now you can use surf2surf or label2label to go to your subjects and
obtain
stats.
Br!
On 27/03/2013, at 05:35, ZhiLiangLong lagosslong1987@163.com wrote:
Hi all;
I need a suface-based aal template which is compatible with FSsurface
file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI
space
onto the surface template (e.g. fsaverage template) in FS. Is it
correct? if
in this case, how can i do the transformation?
Any suggestions appreciated.
Besh wishes.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
freesurfer@nmr.mgh.harvard.edu
-
Garikoitz Lerma-Usabiaga -
Jürgen Hänggi -
Martijn Steenwijk -
MCLAREN, Donald -
Thomas Yeo -
ZhiLiangLong