Hi!
We're attempting to overlay group results (generated in neurolens) on a freesurfer-generated inflated brain (and pial surface) in neurolens. The neurolens administrators previously posted instructions on how to do so, but they have not been updated since freesurfer switched from the cor to mgz file format.
The old instructions say to open the statistical map and the freesurfer-generated surface in neurolens, and then use the info-.COR file generated by freesurfer to convert the surface vertex coordinates to scanner coordinates. Is there an equivalent to that COR file now??
Thanks
-Angela
Hi Angela,
all the information that was in the COR-.info file is now in the .mgz file, so hopefully it should work. We switched a long time ago now, so I would think (hope?) Rick would have gotten around to supporting it.
cheers, Bruce
On Fri, 3 Oct 2008, Fenoglio, Angela J wrote:
Hi!
We're attempting to overlay group results (generated in neurolens) on a freesurfer-generated inflated brain (and pial surface) in neurolens. The neurolens administrators previously posted instructions on how to do so, but they have not been updated since freesurfer switched from the cor to mgz file format.
The old instructions say to open the statistical map and the freesurfer-generated surface in neurolens, and then use the info-.COR file generated by freesurfer to convert the surface vertex coordinates to scanner coordinates. Is there an equivalent to that COR file now??
Thanks
-Angela
Hello,
I have a couple of questions on which I would like to have your opinion.
The first is the voxel resolution impact on cortical thickness sensitivity. I'm using 1.25 mm3 isotropic voxels, and I know that FS interpolates scans to 1mm - is it possible that the 1.25 mm resolution hinders cortical thickness measurements? I'm asking this because I'm analysing an AD cohort whose result seems full of false negatives (I'm in the process of inspecting the intermediate steps as well - I just wanted to check if resolution was a factor as well).
I would also like to know if it is possible (and advisable) to input already optimally skull stripped and bias corrected brains into the recon-all pipeline. If that is possible, I would assume that I need to bypass those steps, and I would like to know which arguments to use in recon-all in order to do so.
Thank you very much for all your help!
Best,
Joao Pereira
João, Here is my opinion:
I have worked on resolutions distinct than 1mm3 isotropic and usually I have no problem. What do you mean by false negatives in your cohort study?
I think you should avoid seeding data with skull striped by other program to the pipeline.
Best Regards,
PPJ
2008/10/3 Joao Pereira jmsp2@wbic.cam.ac.uk
Hello,
I have a couple of questions on which I would like to have your opinion.
The first is the voxel resolution impact on cortical thickness sensitivity. I'm using 1.25 mm3 isotropic voxels, and I know that FS interpolates scans to 1mm - is it possible that the 1.25 mm resolution hinders cortical thickness measurements? I'm asking this because I'm analysing an AD cohort whose result seems full of false negatives (I'm in the process of inspecting the intermediate steps as well - I just wanted to check if resolution was a factor as well).
I would also like to know if it is possible (and advisable) to input already optimally skull stripped and bias corrected brains into the recon-all pipeline. If that is possible, I would assume that I need to bypass those steps, and I would like to know which arguments to use in recon-all in order to do so.
Thank you very much for all your help!
Best,
Joao Pereira
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Pedro,
Thanks for your reply.
By false negatives I mean a lack of detection of atrophic areas which I know are present in this AD cohort, namely the parietal convexities. I'm unable to visualise them with FS.
Finally, you've recommended me not to seed anything to recon-all which had been skull stripped. Is there any way of going around this? And what about data which had been previously bias corrected?
Thank you very much for all you help!
Best,
Joao
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]On Behalf Of Pedro Paulo de Magalhães Oliveira Junior Sent: 03 October 2008 21:25 To: Joao Pereira Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Voxel resolution impact / skull stripping and biascorrection replacement
João,
Here is my opinion:
I have worked on resolutions distinct than 1mm3 isotropic and usually I have no problem. What do you mean by false negatives in your cohort study?
I think you should avoid seeding data with skull striped by other program to the pipeline.
Best Regards,
PPJ
2008/10/3 Joao Pereira jmsp2@wbic.cam.ac.uk
Hello,
I have a couple of questions on which I would like to have your opinion.
The first is the voxel resolution impact on cortical thickness sensitivity. I'm using 1.25 mm3 isotropic voxels, and I know that FS interpolates scans to 1mm - is it possible that the 1.25 mm resolution hinders cortical thickness measurements? I'm asking this because I'm analysing an AD cohort whose result seems full of false negatives (I'm in the process of inspecting the intermediate steps as well - I just wanted to check if resolution was a factor as well).
I would also like to know if it is possible (and advisable) to input already optimally skull stripped and bias corrected brains into the recon-all pipeline. If that is possible, I would assume that I need to bypass those steps, and I would like to know which arguments to use in recon-all in order to do so.
Thank you very much for all your help!
Best,
Joao Pereira
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom
Hi Joao,
previous bias correction should be fine, and previous skull stripping (if it's accurate) should as well, assuming you understand the recon-all stream well enough to get into it at the right place.
As for the false negatives, can you tell us something about your data? What stage of AD? What are you comparing to? We've processed a *ton* of AD data and have seen different things in different cohorts, but some basic patterns repeated.
cheers, Bruce
On Sun, 5 Oct 2008, Joao Pereira wrote:
Pedro,
Thanks for your reply.
By false negatives I mean a lack of detection of atrophic areas which I know are present in this AD cohort, namely the parietal convexities. I'm unable to visualise them with FS.
Finally, you've recommended me not to seed anything to recon-all which had been skull stripped. Is there any way of going around this? And what about data which had been previously bias corrected?
Thank you very much for all you help!
Best,
Joao
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]On Behalf Of Pedro Paulo de Magalhães Oliveira Junior Sent: 03 October 2008 21:25 To: Joao Pereira Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Voxel resolution impact / skull stripping and biascorrection replacement
João,
Here is my opinion:
I have worked on resolutions distinct than 1mm3 isotropic and usually I have no problem. What do you mean by false negatives in your cohort study?
I think you should avoid seeding data with skull striped by other program to the pipeline.
Best Regards,
PPJ
2008/10/3 Joao Pereira jmsp2@wbic.cam.ac.uk
Hello,
I have a couple of questions on which I would like to have your opinion.
The first is the voxel resolution impact on cortical thickness sensitivity. I'm using 1.25 mm3 isotropic voxels, and I know that FS interpolates scans to 1mm - is it possible that the 1.25 mm resolution hinders cortical thickness measurements? I'm asking this because I'm analysing an AD cohort whose result seems full of false negatives (I'm in the process of inspecting the intermediate steps as well - I just wanted to check if resolution was a factor as well).
I would also like to know if it is possible (and advisable) to input already optimally skull stripped and bias corrected brains into the recon-all pipeline. If that is possible, I would assume that I need to bypass those steps, and I would like to know which arguments to use in recon-all in order to do so.
Thank you very much for all your help!
Best,
Joao Pereira
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom
João, As Bruce said different cohort produce different results. You should expect a thinning in superior temporal, in enthorrinal cortex. Sometimes in AD I haven't found thinning in parietal cortex.
But I think you should compare your cohort with the published data with AD and cortical surface analysis (I have an annotated bibliography I can share)
Best Regards,
Pedro Paulo Jr.
2008/10/5 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Joao,
previous bias correction should be fine, and previous skull stripping (if it's accurate) should as well, assuming you understand the recon-all stream well enough to get into it at the right place.
As for the false negatives, can you tell us something about your data? What stage of AD? What are you comparing to? We've processed a *ton* of AD data and have seen different things in different cohorts, but some basic patterns repeated.
cheers, Bruce
On Sun, 5 Oct 2008, Joao Pereira wrote:
Pedro,
Thanks for your reply.
By false negatives I mean a lack of detection of atrophic areas which I know are present in this AD cohort, namely the parietal convexities. I'm unable to visualise them with FS.
Finally, you've recommended me not to seed anything to recon-all which had been skull stripped. Is there any way of going around this? And what about data which had been previously bias corrected?
Thank you very much for all you help!
Best,
Joao
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]On Behalf Of Pedro Paulo de Magalhães Oliveira Junior Sent: 03 October 2008 21:25 To: Joao Pereira Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Voxel resolution impact / skull stripping and biascorrection replacement
João,
Here is my opinion:
I have worked on resolutions distinct than 1mm3 isotropic and usually I have no problem. What do you mean by false negatives in your cohort study?
I think you should avoid seeding data with skull striped by other program to the pipeline.
Best Regards,
PPJ
2008/10/3 Joao Pereira jmsp2@wbic.cam.ac.uk
Hello,
I have a couple of questions on which I would like to have your opinion.
The first is the voxel resolution impact on cortical thickness sensitivity. I'm using 1.25 mm3 isotropic voxels, and I know that FS interpolates scans to 1mm - is it possible that the 1.25 mm resolution hinders cortical thickness measurements? I'm asking this because I'm analysing an AD cohort whose result seems full of false negatives (I'm in the process of inspecting the intermediate steps as well - I just wanted to check if resolution was a factor as well).
I would also like to know if it is possible (and advisable) to input already optimally skull stripped and bias corrected brains into the recon-all pipeline. If that is possible, I would assume that I need to bypass those steps, and I would like to know which arguments to use in recon-all in order to do so.
Thank you very much for all your help!
Best,
Joao Pereira
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Fenoglio, Angela J -
Joao Pereira -
Pedro Paulo de Magalhães Oliveira Junior