Dear FreeSurfer community, I am one of the developers of NeuroVault.org - an open repository for vizualizing, analyzing, and sharing of statistical and parcellation maps of the human brain. So far NeuroVault was limited only to volumetric data in the MNI space since this is the most common way of reporting MRI results. Now I would like to start working on adding support for surface data beginning with outputs of FreeSurfer. Since I'm not a FreeSurfer expert I would like to ask the community a few questions:
1. In NeuroVault users are asked to upload their statistical maps in form of files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but also sig.mgh. Is this the most sensible thing to do?
2. I want to be able to tell if a given map is in fsaverage space. Is there any place in the .mgh header that specifies which space the map is in?
3. fsaverage has different subsampling flavours - how often are they used? Is support for them an important feature?
4. Results come in two files - one per each hemisphere. Is there any way (from the headers) to check if two files provided by a user match?
5. As with the volumetric data I want to provide a 3D interactive viewer. I had some initial success with Brain Browser. Are you aware of any other javascript based viewers that work well with FreeSurfer data?
6. Which surface should be the default view: inflated, pial, or white?
7. Finally NeuroVault gives users ability to compare maps and even search through the whole repository to find statistical maps with similar patterns. This is currently implemented for volumetric data, but could be extended to surface data. The problem arises when one wants to compare MNI volumetric data with fsaverage surface data. So far I have been using mri_vol2surf with target subject being fsaverage (with a supplied affine correction matrix), but this solution is far from optimal since fsaverage folding patterns are quite different from MNI. I was thinking that maybe a more accurate way of dealing with this would be to reconstruct MNI152 cortical surface model, do surface registration of it to fsaverage, and use that to sample statistical maps in MNI space. What do you think?
Thank you for any help feedback you can provide!
Best, Chris Gorgolewski
Hi Chris,
Why not focus on distributing GIFTI files that are viewable both by FreeSurfer and many other applications instead of FreeSurfer¹s native format? For the same reason that it is helpful to provide NIFTI files because of their strong, cross-platform adoption, it would be more helpful to provide GIFTI files in your database so that a wider range of users could use them without converting them. You could probably automatically convert FreeSurfer¹s native formats to GIFTI with FreeSurfer¹s utility mris_convert on upload if you didn¹t want your uploading users to have to do the conversions.
Generally inflated surfaces are easiest for viewing patterns, but it is often helpful to include anatomical surfaces as well.
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Chris Filo Gorgolewski chris.gorgolewski@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Saturday, August 20, 2016 at 12:21 PM To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Support for surface data on NeuroVault.org
Dear FreeSurfer community, I am one of the developers of NeuroVault.org http://NeuroVault.org - an open repository for vizualizing, analyzing, and sharing of statistical and parcellation maps of the human brain. So far NeuroVault was limited only to volumetric data in the MNI space since this is the most common way of reporting MRI results. Now I would like to start working on adding support for surface data beginning with outputs of FreeSurfer. Since I'm not a FreeSurfer expert I would like to ask the community a few questions:
1. In NeuroVault users are asked to upload their statistical maps in form of files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but also sig.mgh. Is this the most sensible thing to do?
2. I want to be able to tell if a given map is in fsaverage space. Is there any place in the .mgh header that specifies which space the map is in?
3. fsaverage has different subsampling flavours - how often are they used? Is support for them an important feature?
4. Results come in two files - one per each hemisphere. Is there any way (from the headers) to check if two files provided by a user match?
5. As with the volumetric data I want to provide a 3D interactive viewer. I had some initial success with Brain Browser. Are you aware of any other javascript based viewers that work well with FreeSurfer data?
6. Which surface should be the default view: inflated, pial, or white?
7. Finally NeuroVault gives users ability to compare maps and even search through the whole repository to find statistical maps with similar patterns. This is currently implemented for volumetric data, but could be extended to surface data. The problem arises when one wants to compare MNI volumetric data with fsaverage surface data. So far I have been using mri_vol2surf with target subject being fsaverage (with a supplied affine correction matrix), but this solution is far from optimal since fsaverage folding patterns are quite different from MNI. I was thinking that maybe a more accurate way of dealing with this would be to reconstruct MNI152 cortical surface model, do surface registration of it to fsaverage, and use that to sample statistical maps in MNI space. What do you think?
Thank you for any help feedback you can provide!
Best, Chris Gorgolewski _______________________________________________ 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.
On Sat, Aug 20, 2016 at 10:39 AM, Matt Glasser matt@ma-tea.com wrote:
Why not focus on distributing GIFTI files that are viewable both by FreeSurfer and many other applications instead of FreeSurfer’s native format? For the same reason that it is helpful to provide NIFTI files because of their strong, cross-platform adoption, it would be more helpful to provide GIFTI files in your database so that a wider range of users could use them without converting them. You could probably automatically convert FreeSurfer’s native formats to GIFTI with FreeSurfer’s utility mris_convert on upload if you didn’t want your uploading users to have to do the conversions.
I was merely discussing the format required for the upload - which I want to keep as straightforward as possible for the users. As you mentioned we can do a conversion server side and provide other file formats. Having an optional download the data as gifti might be very useful. Would that be a "Functional" gifti file? So .func.gii? This does not seem right since many statistical maps will come from anatomical data. I cannot find the right intent in the GIFTI spec (section 13): it's not a set of coordinates, neither a label map... How are statistical maps usually stored in gifti?
Would we also need to provide each map in .mgh or is .gii sufficient for FreeSurfer users? Is displaying statistical map overlay coming in a form of a .gii file easy in FreeView? What about pysurfer?
Generally inflated surfaces are easiest for viewing patterns, but it is
often helpful to include anatomical surfaces as well.
Thanks!
Best, Chris
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Chris Filo Gorgolewski chris.gorgolewski@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Saturday, August 20, 2016 at 12:21 PM To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Support for surface data on NeuroVault.org
Dear FreeSurfer community, I am one of the developers of NeuroVault.org - an open repository for vizualizing, analyzing, and sharing of statistical and parcellation maps of the human brain. So far NeuroVault was limited only to volumetric data in the MNI space since this is the most common way of reporting MRI results. Now I would like to start working on adding support for surface data beginning with outputs of FreeSurfer. Since I'm not a FreeSurfer expert I would like to ask the community a few questions:
- In NeuroVault users are asked to upload their statistical maps in form
of files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but also sig.mgh. Is this the most sensible thing to do?
- I want to be able to tell if a given map is in fsaverage space. Is
there any place in the .mgh header that specifies which space the map is in?
- fsaverage has different subsampling flavours - how often are they used?
Is support for them an important feature?
- Results come in two files - one per each hemisphere. Is there any way
(from the headers) to check if two files provided by a user match?
- As with the volumetric data I want to provide a 3D interactive viewer.
I had some initial success with Brain Browser. Are you aware of any other javascript based viewers that work well with FreeSurfer data?
Which surface should be the default view: inflated, pial, or white?
Finally NeuroVault gives users ability to compare maps and even search
through the whole repository to find statistical maps with similar patterns. This is currently implemented for volumetric data, but could be extended to surface data. The problem arises when one wants to compare MNI volumetric data with fsaverage surface data. So far I have been using mri_vol2surf with target subject being fsaverage (with a supplied affine correction matrix), but this solution is far from optimal since fsaverage folding patterns are quite different from MNI. I was thinking that maybe a more accurate way of dealing with this would be to reconstruct MNI152 cortical surface model, do surface registration of it to fsaverage, and use that to sample statistical maps in MNI space. What do you think?
Thank you for any help feedback you can provide!
Best, Chris Gorgolewski _______________________________________________ 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.
GIFTI has two identical formats for scalar (e.g. Statistical) data. .func.gii and .shape.gii are basically identical. It is also a good idea to provide some surfaces upon which to display the GIFTI data.
I¹m a bit puzzled as to how to display arbitrary scalar overlays at all in FreeView (though I figured out how to display label/annot files which worked fine as GIFTI). I don¹t know anything about pysurfer.
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Chris Filo Gorgolewski chris.gorgolewski@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Saturday, August 20, 2016 at 1:51 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Support for surface data on NeuroVault.org
On Sat, Aug 20, 2016 at 10:39 AM, Matt Glasser matt@ma-tea.com wrote:
Why not focus on distributing GIFTI files that are viewable both by FreeSurfer and many other applications instead of FreeSurfer¹s native format? For the same reason that it is helpful to provide NIFTI files because of their strong, cross-platform adoption, it would be more helpful to provide GIFTI files in your database so that a wider range of users could use them without converting them. You could probably automatically convert FreeSurfer¹s native formats to GIFTI with FreeSurfer¹s utility mris_convert on upload if you didn¹t want your uploading users to have to do the conversions.
I was merely discussing the format required for the upload - which I want to keep as straightforward as possible for the users. As you mentioned we can do a conversion server side and provide other file formats. Having an optional download the data as gifti might be very useful. Would that be a "Functional" gifti file? So .func.gii? This does not seem right since many statistical maps will come from anatomical data. I cannot find the right intent in the GIFTI spec (section 13): it's not a set of coordinates, neither a label map... How are statistical maps usually stored in gifti?
Would we also need to provide each map in .mgh or is .gii sufficient for FreeSurfer users? Is displaying statistical map overlay coming in a form of a .gii file easy in FreeView? What about pysurfer?
Generally inflated surfaces are easiest for viewing patterns, but it is often helpful to include anatomical surfaces as well.
Thanks!
Best, Chris
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Chris Filo Gorgolewski chris.gorgolewski@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Saturday, August 20, 2016 at 12:21 PM To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Support for surface data on NeuroVault.org
Dear FreeSurfer community, I am one of the developers of NeuroVault.org http://NeuroVault.org - an open repository for vizualizing, analyzing, and sharing of statistical and parcellation maps of the human brain. So far NeuroVault was limited only to volumetric data in the MNI space since this is the most common way of reporting MRI results. Now I would like to start working on adding support for surface data beginning with outputs of FreeSurfer. Since I'm not a FreeSurfer expert I would like to ask the community a few questions:
- In NeuroVault users are asked to upload their statistical maps in form of
files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but also sig.mgh. Is this the most sensible thing to do?
- I want to be able to tell if a given map is in fsaverage space. Is there
any place in the .mgh header that specifies which space the map is in?
- fsaverage has different subsampling flavours - how often are they used? Is
support for them an important feature?
- Results come in two files - one per each hemisphere. Is there any way (from
the headers) to check if two files provided by a user match?
- As with the volumetric data I want to provide a 3D interactive viewer. I
had some initial success with Brain Browser. Are you aware of any other javascript based viewers that work well with FreeSurfer data?
Which surface should be the default view: inflated, pial, or white?
Finally NeuroVault gives users ability to compare maps and even search
through the whole repository to find statistical maps with similar patterns. This is currently implemented for volumetric data, but could be extended to surface data. The problem arises when one wants to compare MNI volumetric data with fsaverage surface data. So far I have been using mri_vol2surf with target subject being fsaverage (with a supplied affine correction matrix), but this solution is far from optimal since fsaverage folding patterns are quite different from MNI. I was thinking that maybe a more accurate way of dealing with this would be to reconstruct MNI152 cortical surface model, do surface registration of it to fsaverage, and use that to sample statistical maps in MNI space. What do you think?
Thank you for any help feedback you can provide!
Best, Chris Gorgolewski _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinf o/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.
On 08/20/2016 01:21 PM, Chris Filo Gorgolewski wrote:
Dear FreeSurfer community, I am one of the developers of NeuroVault.org http://NeuroVault.org - an open repository for vizualizing, analyzing, and sharing of statistical and parcellation maps of the human brain. So far NeuroVault was limited only to volumetric data in the MNI space since this is the most common way of reporting MRI results. Now I would like to start working on adding support for surface data beginning with outputs of FreeSurfer. Since I'm not a FreeSurfer expert I would like to ask the community a few questions:
- In NeuroVault users are asked to upload their statistical maps in
form of files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but also sig.mgh. Is this the most sensible thing to do?
Yes. You may also want the gamma.mgh file as that is the size of the effect (eg, thickness change in mm )
- I want to be able to tell if a given map is in fsaverage space. Is
there any place in the .mgh header that specifies which space the map is in?
No.
- fsaverage has different subsampling flavours - how often are they
used? Is support for them an important feature?
Not very often. I would probably not worry about it.
- Results come in two files - one per each hemisphere. Is there any
way (from the headers) to check if two files provided by a user match?
match in what way? There is nothing in the mgh file to indicate laterality.
- As with the volumetric data I want to provide a 3D interactive
viewer. I had some initial success with Brain Browser. Are you aware of any other javascript based viewers that work well with FreeSurfer data?
I'm not, but I'm not the best person to ask.
- Which surface should be the default view: inflated, pial, or white?
I always to with pial with the aparc outlines. Others may feel differently.
- Finally NeuroVault gives users ability to compare maps and even
search through the whole repository to find statistical maps with similar patterns. This is currently implemented for volumetric data, but could be extended to surface data. The problem arises when one wants to compare MNI volumetric data with fsaverage surface data. So far I have been using mri_vol2surf with target subject being fsaverage (with a supplied affine correction matrix), but this solution is far from optimal since fsaverage folding patterns are quite different from MNI. I was thinking that maybe a more accurate way of dealing with this would be to reconstruct MNI152 cortical surface model, do surface registration of it to fsaverage, and use that to sample statistical maps in MNI space. What do you think?
I would probably go the other direction, ie, sample the MNI152 maps into surface space.
Thank you for any help feedback you can provide!
Best, Chris Gorgolewski
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you for your comments. Some more questions below:
On Mon, Aug 22, 2016 at 1:09 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
- In NeuroVault users are asked to upload their statistical maps in
form of files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but also sig.mgh. Is this the most sensible thing to do?
Yes. You may also want the gamma.mgh file as that is the size of the effect (eg, thickness change in mm )
This would be very useful - an effect size in meaningful units is a rarity in neuroimaging!
- Finally NeuroVault gives users ability to compare maps and even
search through the whole repository to find statistical maps with similar patterns. This is currently implemented for volumetric data, but could be extended to surface data. The problem arises when one wants to compare MNI volumetric data with fsaverage surface data. So far I have been using mri_vol2surf with target subject being fsaverage (with a supplied affine correction matrix), but this solution is far from optimal since fsaverage folding patterns are quite different from MNI. I was thinking that maybe a more accurate way of dealing with this would be to reconstruct MNI152 cortical surface model, do surface registration of it to fsaverage, and use that to sample statistical maps in MNI space. What do you think?
I would probably go the other direction, ie, sample the MNI152 maps into surface space.
This is exactly what I want to do. The question is what is the most accurate way of sampling MNI152 maps to fsaverage?
Best, Chris
Thank you for any help feedback you can provide!
Best, Chris Gorgolewski
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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/
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
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Chris Filo Gorgolewski -
Douglas N Greve -
Matt Glasser