Hi,
many thanks for your help! Unfortunately, I still have some questions:
1) Why would someone only want to display the results on a cohort-specific average, but not use that average for calculation?
2) So if I want to use my cohort-specific average for calcuation of the cortical thickness and I registered all subjects on that, do I then still have to calculate a newnew make_average_subject as it is described on the SurfaceRegAndTemplated page? What is the reason behind that? If I should do it, what flags would mris_preproc need: the --target newnewtemplate and the surfreg newtemplate.sphere.reg?
Best wishes, Christina
_______________________________________ Von: Douglas N Greve [greve@nmr.mgh.harvard.edu] Gesendet: Freitag, 1. Juni 2012 17:44 An: Bruce Fischl Cc: Schuster, Christina /DZNE Betreff: Re: AW: [Freesurfer] using own average subject
If all you want to do is display it on your average subject, then you can pass fsaverage to mris_preproc and then just display it on your cohort-specific average. doug
On 06/01/2012 11:37 AM, Douglas N Greve wrote:
Hi Christina, if you want to use the registration to your new template, then you need to run mris_register on each subject to register to the new template. You can actually do this with surfreg, something like:
foreach subject (subj1 subj2) surfreg --s $subject --t newtemplate --lh end
This will create $subject/surf/lh.newtemplate.sphere.reg
You can then run
mris_preproc --target newtemplate --surfreg newtemplate.sphere.reg ...
Note that the surfreg cmd above will take about an hour for each subject
doug
On 06/01/2012 11:05 AM, Bruce Fischl wrote:
Hi Christina
you should cc the list so others (Doug!) can answer. The purpose of mris_register is to bring your subjects into a common surface-based coordinate system. fsaverage lives in that space, but so will the average that you make
cheers Bruce
On Fri, 1 Jun 2012, Schuster, Christina /DZNE wrote:
Hi Bruce,
just to be sure that I understood it correctly:
I just use make_average_subject to create my template and then I use mris_preproc --target newtemplate and not further --surf-reg specification. Then after mri_glmfit --surf newtemplate ... I have my final results?!
So what is the purpose of the mris_register command?
Many thanks for your help. Best wishes Christina
Von: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 31. Mai 2012 20:39 An: Schuster, Christina /DZNE Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] using own average subject
Hi Christina,
the new template will already be in the same target space as fsaverage since you used the sphere.reg to create it. Just use it as a background for your group results.
cheers Bruce
On Thu, 31 May 2012, Schuster, Christina /DZNE wrote:
Dear FreeSurfer experts,
I am trying to create an average subject based on a matched subsample (2 different scanners, patients and healthy controls).
I successfully ran make_average_subject receiving a "newtemplate". Now I am unsure how to proceed:
As far as I understand it, according to the SurfaceRegAndTemplates page (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates) I should use mris_register for each subject from my subsample receiving ?h.sphere.reg.newtemple files with which I should make again an average subject, let's call it "newnewtemplate".
Is that correct?
Now, if I want to assemble the data into common space using mris_preproc: what do I need to specify? Would --target be the newtemplate or newnewtemplate? Do I need to specifiy the --surf-reg as well?
On the other hand, I read in one of your tutorials that I only need to run make_average_subject receiving a "newtemplate" which I then specify using mris_preproc as --target and that --surf-reg is not needed.
So what would be the correct way to use my own template for the group analysis?
Many thanks for you help!
Best wishes Christina
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.
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Hi Christina,
1. Displaying data on your own subjects average can be less misleading than on our's, particularly if you don't have many subjects. It shows at least one measure of the true variability/accuracy of the registration of your subjects.
2. To make a study-specific target for the spherical registration you would need to use mris_make_template to create a .tif file as a target, then rerun mris_register to register to it. Then rerun make_average_subject and all the statisticaly analyses using the new spherical registrations.
cheers Bruce
On Mon, 4 Jun 2012, Schuster, Christina /DZNE wrote:
Hi,
many thanks for your help! Unfortunately, I still have some questions:
Why would someone only want to display the results on a cohort-specific average, but not use that average for calculation?
So if I want to use my cohort-specific average for calcuation of the
cortical thickness and I registered all subjects on that, do I then still have to calculate a newnew make_average_subject as it is described on the SurfaceRegAndTemplated page? What is the reason behind that?
If I should do it, what flags would mris_preproc need: the --target newnewtemplate and the surfreg newtemplate.sphere.reg?
Best wishes, Christina
Von: Douglas N Greve [greve@nmr.mgh.harvard.edu] Gesendet: Freitag, 1. Juni 2012 17:44 An: Bruce Fischl Cc: Schuster, Christina /DZNE Betreff: Re: AW: [Freesurfer] using own average subject
If all you want to do is display it on your average subject, then you can pass fsaverage to mris_preproc and then just display it on your cohort-specific average. doug
On 06/01/2012 11:37 AM, Douglas N Greve wrote:
Hi Christina, if you want to use the registration to your new template, then you need to run mris_register on each subject to register to the new template. You can actually do this with surfreg, something like:
foreach subject (subj1 subj2) surfreg --s $subject --t newtemplate --lh end
This will create $subject/surf/lh.newtemplate.sphere.reg
You can then run
mris_preproc --target newtemplate --surfreg newtemplate.sphere.reg ...
Note that the surfreg cmd above will take about an hour for each subject
doug
On 06/01/2012 11:05 AM, Bruce Fischl wrote:
Hi Christina
you should cc the list so others (Doug!) can answer. The purpose of mris_register is to bring your subjects into a common surface-based coordinate system. fsaverage lives in that space, but so will the average that you make
cheers Bruce
On Fri, 1 Jun 2012, Schuster, Christina /DZNE wrote:
Hi Bruce,
just to be sure that I understood it correctly:
I just use make_average_subject to create my template and then I use mris_preproc --target newtemplate and not further --surf-reg specification. Then after mri_glmfit --surf newtemplate ... I have my final results?!
So what is the purpose of the mris_register command?
Many thanks for your help. Best wishes Christina
Von: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 31. Mai 2012 20:39 An: Schuster, Christina /DZNE Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] using own average subject
Hi Christina,
the new template will already be in the same target space as fsaverage since you used the sphere.reg to create it. Just use it as a background for your group results.
cheers Bruce
On Thu, 31 May 2012, Schuster, Christina /DZNE wrote:
Dear FreeSurfer experts,
I am trying to create an average subject based on a matched subsample (2 different scanners, patients and healthy controls).
I successfully ran make_average_subject receiving a "newtemplate". Now I am unsure how to proceed:
As far as I understand it, according to the SurfaceRegAndTemplates page (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates) I should use mris_register for each subject from my subsample receiving ?h.sphere.reg.newtemple files with which I should make again an average subject, let's call it "newnewtemplate".
Is that correct?
Now, if I want to assemble the data into common space using mris_preproc: what do I need to specify? Would --target be the newtemplate or newnewtemplate? Do I need to specifiy the --surf-reg as well?
On the other hand, I read in one of your tutorials that I only need to run make_average_subject receiving a "newtemplate" which I then specify using mris_preproc as --target and that --surf-reg is not needed.
So what would be the correct way to use my own template for the group analysis?
Many thanks for you help!
Best wishes Christina
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.
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
For #2, make_average_subject will create the .tif file in the output directory. doug
On 06/04/2012 09:06 AM, Bruce Fischl wrote:
Hi Christina,
- Displaying data on your own subjects average can be less misleading
than on our's, particularly if you don't have many subjects. It shows at least one measure of the true variability/accuracy of the registration of your subjects.
- To make a study-specific target for the spherical registration you
would need to use mris_make_template to create a .tif file as a target, then rerun mris_register to register to it. Then rerun make_average_subject and all the statisticaly analyses using the new spherical registrations.
cheers Bruce
On Mon, 4 Jun 2012, Schuster, Christina /DZNE wrote:
Hi,
many thanks for your help! Unfortunately, I still have some questions:
- Why would someone only want to display the results on a
cohort-specific average, but not use that average for calculation?
- So if I want to use my cohort-specific average for calcuation of the
cortical thickness and I registered all subjects on that, do I then still have to calculate a newnew make_average_subject as it is described on the SurfaceRegAndTemplated page? What is the reason behind that?
If I should do it, what flags would mris_preproc need: the --target newnewtemplate and the surfreg newtemplate.sphere.reg?
Best wishes, Christina
Von: Douglas N Greve [greve@nmr.mgh.harvard.edu] Gesendet: Freitag, 1. Juni 2012 17:44 An: Bruce Fischl Cc: Schuster, Christina /DZNE Betreff: Re: AW: [Freesurfer] using own average subject
If all you want to do is display it on your average subject, then you can pass fsaverage to mris_preproc and then just display it on your cohort-specific average. doug
On 06/01/2012 11:37 AM, Douglas N Greve wrote:
Hi Christina, if you want to use the registration to your new template, then you need to run mris_register on each subject to register to the new template. You can actually do this with surfreg, something like:
foreach subject (subj1 subj2) surfreg --s $subject --t newtemplate --lh end
This will create $subject/surf/lh.newtemplate.sphere.reg
You can then run
mris_preproc --target newtemplate --surfreg newtemplate.sphere.reg ...
Note that the surfreg cmd above will take about an hour for each subject
doug
On 06/01/2012 11:05 AM, Bruce Fischl wrote:
Hi Christina
you should cc the list so others (Doug!) can answer. The purpose of mris_register is to bring your subjects into a common surface-based coordinate system. fsaverage lives in that space, but so will the average that you make
cheers Bruce
On Fri, 1 Jun 2012, Schuster, Christina /DZNE wrote:
Hi Bruce,
just to be sure that I understood it correctly:
I just use make_average_subject to create my template and then I use mris_preproc --target newtemplate and not further --surf-reg specification. Then after mri_glmfit --surf newtemplate ... I have my final results?!
So what is the purpose of the mris_register command?
Many thanks for your help. Best wishes Christina
Von: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 31. Mai 2012 20:39 An: Schuster, Christina /DZNE Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] using own average subject
Hi Christina,
the new template will already be in the same target space as fsaverage since you used the sphere.reg to create it. Just use it as a background for your group results.
cheers Bruce
On Thu, 31 May 2012, Schuster, Christina /DZNE wrote:
Dear FreeSurfer experts,
I am trying to create an average subject based on a matched subsample (2 different scanners, patients and healthy controls).
I successfully ran make_average_subject receiving a "newtemplate". Now I am unsure how to proceed:
As far as I understand it, according to the SurfaceRegAndTemplates page (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates) I should use mris_register for each subject from my subsample receiving ?h.sphere.reg.newtemple files with which I should make again an average subject, let's call it "newnewtemplate".
Is that correct?
Now, if I want to assemble the data into common space using mris_preproc: what do I need to specify? Would --target be the newtemplate or newnewtemplate? Do I need to specifiy the --surf-reg as well?
On the other hand, I read in one of your tutorials that I only need to run make_average_subject receiving a "newtemplate" which I then specify using mris_preproc as --target and that --surf-reg is not needed.
So what would be the correct way to use my own template for the group analysis?
Many thanks for you help!
Best wishes Christina
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.
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Hi,
what would you consider a small sample? I have one sample of 40 participants (20 patients, 20 controls) for that I thought it would be best to use the fsaverage and then maybe display it on my own subjects average.
The other study consists of roughly 140 participants (1/3 are healthy controls) measured by 2 different scanners. The age range is from 30 to 80 years. Would you recommand to make an own subjects average template for that sample? According to the SurfaceRegAndTemplates page, if I want to calculate the template one particular subject is used for the starting point. Do I have to choose that particular subject? How do I do that best? Would the analysis still be valid if I simply use the fsaverage? Eventually, I am going to analyse longitundinal data of these subjects. I am not sure whether this may influence the decision whether or not to calculate an own template.
Many thanks for you help Cheers, Christina
________________________________________ Von: Douglas N Greve [greve@nmr.mgh.harvard.edu] Gesendet: Montag, 4. Juni 2012 16:04 An: Bruce Fischl Cc: Schuster, Christina /DZNE; freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: AW: [Freesurfer] using own average subject
For #2, make_average_subject will create the .tif file in the output directory. doug
On 06/04/2012 09:06 AM, Bruce Fischl wrote:
Hi Christina,
- Displaying data on your own subjects average can be less misleading
than on our's, particularly if you don't have many subjects. It shows at least one measure of the true variability/accuracy of the registration of your subjects.
- To make a study-specific target for the spherical registration you
would need to use mris_make_template to create a .tif file as a target, then rerun mris_register to register to it. Then rerun make_average_subject and all the statisticaly analyses using the new spherical registrations.
cheers Bruce
On Mon, 4 Jun 2012, Schuster, Christina /DZNE wrote:
Hi,
many thanks for your help! Unfortunately, I still have some questions:
- Why would someone only want to display the results on a
cohort-specific average, but not use that average for calculation?
- So if I want to use my cohort-specific average for calcuation of the
cortical thickness and I registered all subjects on that, do I then still have to calculate a newnew make_average_subject as it is described on the SurfaceRegAndTemplated page? What is the reason behind that?
If I should do it, what flags would mris_preproc need: the --target newnewtemplate and the surfreg newtemplate.sphere.reg?
Best wishes, Christina
Von: Douglas N Greve [greve@nmr.mgh.harvard.edu] Gesendet: Freitag, 1. Juni 2012 17:44 An: Bruce Fischl Cc: Schuster, Christina /DZNE Betreff: Re: AW: [Freesurfer] using own average subject
If all you want to do is display it on your average subject, then you can pass fsaverage to mris_preproc and then just display it on your cohort-specific average. doug
On 06/01/2012 11:37 AM, Douglas N Greve wrote:
Hi Christina, if you want to use the registration to your new template, then you need to run mris_register on each subject to register to the new template. You can actually do this with surfreg, something like:
foreach subject (subj1 subj2) surfreg --s $subject --t newtemplate --lh end
This will create $subject/surf/lh.newtemplate.sphere.reg
You can then run
mris_preproc --target newtemplate --surfreg newtemplate.sphere.reg ...
Note that the surfreg cmd above will take about an hour for each subject
doug
On 06/01/2012 11:05 AM, Bruce Fischl wrote:
Hi Christina
you should cc the list so others (Doug!) can answer. The purpose of mris_register is to bring your subjects into a common surface-based coordinate system. fsaverage lives in that space, but so will the average that you make
cheers Bruce
On Fri, 1 Jun 2012, Schuster, Christina /DZNE wrote:
Hi Bruce,
just to be sure that I understood it correctly:
I just use make_average_subject to create my template and then I use mris_preproc --target newtemplate and not further --surf-reg specification. Then after mri_glmfit --surf newtemplate ... I have my final results?!
So what is the purpose of the mris_register command?
Many thanks for your help. Best wishes Christina
Von: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 31. Mai 2012 20:39 An: Schuster, Christina /DZNE Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] using own average subject
Hi Christina,
the new template will already be in the same target space as fsaverage since you used the sphere.reg to create it. Just use it as a background for your group results.
cheers Bruce
On Thu, 31 May 2012, Schuster, Christina /DZNE wrote:
Dear FreeSurfer experts,
I am trying to create an average subject based on a matched subsample (2 different scanners, patients and healthy controls).
I successfully ran make_average_subject receiving a "newtemplate". Now I am unsure how to proceed:
As far as I understand it, according to the SurfaceRegAndTemplates page (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates) I should use mris_register for each subject from my subsample receiving ?h.sphere.reg.newtemple files with which I should make again an average subject, let's call it "newnewtemplate".
Is that correct?
Now, if I want to assemble the data into common space using mris_preproc: what do I need to specify? Would --target be the newtemplate or newnewtemplate? Do I need to specifiy the --surf-reg as well?
On the other hand, I read in one of your tutorials that I only need to run make_average_subject receiving a "newtemplate" which I then specify using mris_preproc as --target and that --surf-reg is not needed.
So what would be the correct way to use my own template for the group analysis?
Many thanks for you help!
Best wishes Christina
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.
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Schuster, Christina /DZNE