External Email - Use Caution

The appropriate GIFTI extension for that would be .func.gii. What fsaverage# space is that? Hopefully FreeSurfer provides a tool to convert that to GIFTI in full resolution fsaverage space and from there we can help you get it to CIFTI in fs_LR.

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Katsumi, Yuta" YKATSUMI@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 18, 2020 at 10:43 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

Hi Matt,

For instance, I have a statistical map (e.g., showing magnitude of functional connectivity at each vertex) that has been computed in 16k fsaverage space that I want to display on a fs_LR surface. I was wondering if there’s a way to convert this file (which is in .mgh extension now) to .dscalar so it’d be CIFTI/wb compatible.

Thanks, Yuta

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Glasser, Matthew" glasserm@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 18, 2020 at 10:37 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

External Email - Use Caution What kind of data does one display in an “OVERLAY” file?

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Katsumi, Yuta" YKATSUMI@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 18, 2020 at 5:43 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

Dear FreeSurfer community,

I would like to be able to display OVERLAY files generated in FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states in their documentation (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFA...) that any surfaces to be converted to fs_LR need to be in .gii first, but I know mris_convert doesn’t take overlay files as input. It would be great if you could please let me know how I might be able to achieve this task.

Thanks, Yuta

________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

External Email - Use Caution

Is GIFTI a legal output type for mri_convert? I though it only could be outputted by mris_convert (which does appear to allow .mgh and .gii).

Matt.

On 6/19/20, 8:00 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ts+ml@rcmd.org> wrote:

* External Email - Caution *

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the full 162k fsaverage mesh, but once you have the full fsaverage version, to convert to gifti, just do:

mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew" glasserm@wustl.edu wrote: > > > External Email - Use Caution > > The appropriate GIFTI extension for that would be .func.gii. What fsaverage# space is that? Hopefully FreeSurfer provides a tool to convert that to GIFTI in full resolution fsaverage space and from there we can help you get it to CIFTI in fs_LR. > > Matt. > > From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Katsumi, Yuta" YKATSUMI@mgh.harvard.edu > Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Date: Thursday, June 18, 2020 at 10:43 PM > To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format > > > Hi Matt, > > For instance, I have a statistical map (e.g., showing magnitude of functional connectivity at each vertex) that has been computed in 16k fsaverage space that I want to display on a fs_LR surface. I was wondering if there’s a way to convert this file (which is in .mgh extension now) to .dscalar so it’d be CIFTI/wb compatible. > > Thanks, > Yuta > > From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Glasser, Matthew" glasserm@wustl.edu > Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Date: Thursday, June 18, 2020 at 10:37 PM > To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format > > > External Email - Use Caution > What kind of data does one display in an “OVERLAY” file? > > Matt. > > From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Katsumi, Yuta" YKATSUMI@mgh.harvard.edu > Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Date: Thursday, June 18, 2020 at 5:43 PM > To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format > > > Dear FreeSurfer community, > > I would like to be able to display OVERLAY files generated in FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states in their documentation (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFA...) that any surfaces to be converted to fs_LR need to be in .gii first, but I know mris_convert doesn’t take overlay files as input. It would be great if you could please let me know how I might be able to achieve this task. > > Thanks, > Yuta > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

In general almost all of our binaries will read or write almost all formats we support. There are some exceptions to this, but it is generally true

Cheers Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Katsumi, Yuta Sent: Friday, June 19, 2020 9:42 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

Thanks, Tim and Matt. I made a typo earlier - I meant to say that my overlay files are already in full fsaverage space with ~164k vertices.

I also thought that mri_convert doesn’t take .gii as output, but the command that Tim suggested below does indeed seem to work.

Thanks, Yuta

On 6/19/20, 9:05 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Glasser, Matthew" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of glasserm@wustl.edu> wrote:

External Email - Use Caution

Is GIFTI a legal output type for mri_convert? I though it only could be outputted by mris_convert (which does appear to allow .mgh and .gii).

Matt.

On 6/19/20, 8:00 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ts+ml@rcmd.org> wrote:

* External Email - Caution *

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the full 162k fsaverage mesh, but once you have the full fsaverage version, to convert to gifti, just do:

mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew" glasserm@wustl.edu wrote: > > > External Email - Use Caution > > The appropriate GIFTI extension for that would be .func.gii. What fsaverage# space is that? Hopefully FreeSurfer provides a tool to convert that to GIFTI in full resolution fsaverage space and from there we can help you get it to CIFTI in fs_LR. > > Matt. > > From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Katsumi, Yuta" YKATSUMI@mgh.harvard.edu > Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Date: Thursday, June 18, 2020 at 10:43 PM > To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format > > > Hi Matt, > > For instance, I have a statistical map (e.g., showing magnitude of functional connectivity at each vertex) that has been computed in 16k fsaverage space that I want to display on a fs_LR surface. I was wondering if there’s a way to convert this file (which is in .mgh extension now) to .dscalar so it’d be CIFTI/wb compatible. > > Thanks, > Yuta > > From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Glasser, Matthew" glasserm@wustl.edu > Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Date: Thursday, June 18, 2020 at 10:37 PM > To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format > > > External Email - Use Caution > What kind of data does one display in an “OVERLAY” file? > > Matt. > > From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Katsumi, Yuta" YKATSUMI@mgh.harvard.edu > Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Date: Thursday, June 18, 2020 at 5:43 PM > To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format > > > Dear FreeSurfer community, > > I would like to be able to display OVERLAY files generated in FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states in their documentation (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFA...) that any surfaces to be converted to fs_LR need to be in .gii first, but I know mris_convert doesn’t take overlay files as input. It would be great if you could please let me know how I might be able to achieve this task. > > Thanks, > Yuta > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Great, thanks so much again for your input, Matt/Tim/Bruce.

Yuta

On 6/19/20, 1:37 PM, "Glasser, Matthew" glasserm@wustl.edu wrote:

External Email - Use Caution

After you convert to GIFTI at fsaverage 164k, you can use these instructions to get to fs_LR:

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&a...

Matt.

On 6/19/20, 10:04 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of BFISCHL@mgh.harvard.edu> wrote:

* External Email - Caution *

In general almost all of our binaries will read or write almost all formats we support. There are some exceptions to this, but it is generally true

Cheers Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Katsumi, Yuta Sent: Friday, June 19, 2020 9:42 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

Thanks, Tim and Matt. I made a typo earlier - I meant to say that my overlay files are already in full fsaverage space with ~164k vertices.

I also thought that mri_convert doesn’t take .gii as output, but the command that Tim suggested below does indeed seem to work.

Thanks, Yuta

On 6/19/20, 9:05 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Glasser, Matthew" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of glasserm@wustl.edu> wrote:

External Email - Use Caution

Is GIFTI a legal output type for mri_convert? I though it only could be outputted by mris_convert (which does appear to allow .mgh and .gii).

Matt.

On 6/19/20, 8:00 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ts+ml@rcmd.org> wrote:

* External Email - Caution *

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the full 162k fsaverage mesh, but once you have the full fsaverage version, to convert to gifti, just do:

mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew" glasserm@wustl.edu wrote: > > > External Email - Use Caution > > The appropriate GIFTI extension for that would be .func.gii. What fsaverage# space is that? Hopefully FreeSurfer provides a tool to convert that to GIFTI in full resolution fsaverage space and from there we can help you get it to CIFTI in fs_LR. > > Matt. > > From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Katsumi, Yuta" YKATSUMI@mgh.harvard.edu > Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Date: Thursday, June 18, 2020 at 10:43 PM > To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format > > > Hi Matt, > > For instance, I have a statistical map (e.g., showing magnitude of functional connectivity at each vertex) that has been computed in 16k fsaverage space that I want to display on a fs_LR surface. I was wondering if there’s a way to convert this file (which is in .mgh extension now) to .dscalar so it’d be CIFTI/wb compatible. > > Thanks, > Yuta > > From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Glasser, Matthew" glasserm@wustl.edu > Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Date: Thursday, June 18, 2020 at 10:37 PM > To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format > > > External Email - Use Caution > What kind of data does one display in an “OVERLAY” file? > > Matt. > > From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Katsumi, Yuta" YKATSUMI@mgh.harvard.edu > Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Date: Thursday, June 18, 2020 at 5:43 PM > To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format > > > Dear FreeSurfer community, > > I would like to be able to display OVERLAY files generated in FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states in their documentation (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFA...) that any surfaces to be converted to fs_LR need to be in .gii first, but I know mris_convert doesn’t take overlay files as input. It would be great if you could please let me know how I might be able to achieve this task. > > Thanks, > Yuta > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer