You need to map the mask into the fsaverage space. Probably the easiest way to do this is to run recon-all on your template to get surfaces. Then run mri_vol2surf to map your mask onto the surface, then use mris_apply_reg to map your surface mask to fsaverage (make sure to --no-rev since you are mapping a mask). If you want to do FDR, then run mri_fdr.

On 1/29/18 12:17 PM, Charlotte Grosse Wiesmann wrote:

Dear freesurfer experts,

I would like to restrict my surface analyses (cortical thickness and surface area) to a mask from an fMRI meta-analysis using my own subject-specific template that I created with ANTS. So far, I have used Qdec and wanted to correct for cluster size running the Monte Carlo (MC) simulation on my own template. Now I would like to restrict the simulation to my mask to do a small volume correction in my regions of interest. I mapped the mask to my own template (in volume space) using ANTS (WarpImageMultiTransform) but how can I get this mask to the surface space to run the MC simulation on my own template within this mask?

I was planning to do: mri_mcsim --o my_template/mult-comp-cor/my_template/lh/mymask --base mc-z --surface my_template ?h --nreps 10000 --mask mymask.mgz

How do I get mymask.mgz in the correct space for this?

And can I continue using Qdec or do I have to use glmfit for these analyses?

In addition: is it also possible to do a small volume correction using FDR rather than cluster-size correction?

Thanks for your help!

Charlotte _______________________________________________ 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

Hi Doug,

I was trying to map my volume mask from my study-specific average subject template space to the surface (still in my average subject template space) with mri_vol2surf as you suggested below. How d I get the correct register.dat file do do this?

I have tried bbregister but am not sure what subject and what moveable volume I need to take since I am basically staying in the same space (my own average subject space).

I am stuck with my analysis on this and would highly appreciate your help!

Thank you very much in advance!

Charlotte

----- Original Message ----- From: "wiesmann" wiesmann@cbs.mpg.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Friday, February 9, 2018 7:45:35 PM Subject: Re: [Freesurfer] REPOST: mri_mcsim with mask - How do I map a volume mask to the surface space for mri_mcsim using my own template?

Hi Doug,

thank you very much for your help! I am sorry for the naive questions, but I am not very familiar with surface analyses: I ran recon-all on my template ("ANTSaverage") so that I have the surfaces. Is it correct that I have registered my volume mask to my template space before I map it onto the surface with mri_vol2surf? And where do I get the registration file from to run mri_vol2surf?

I am also not quite sure I understand why I have to register the surface mask to fsaverage then rather than to my own template?

I am sorry for these questions, but I am a bit confused and would really appreciate your help!

Charlotte

----- Original Message ----- From: "Douglas Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Saturday, February 3, 2018 8:58:49 PM Subject: Re: [Freesurfer] REPOST: mri_mcsim with mask - How do I map a volume mask to the surface space for mri_mcsim using my own template?

You need to map the mask into the fsaverage space. Probably the easiest way to do this is to run recon-all on your template to get surfaces. Then run mri_vol2surf to map your mask onto the surface, then use mris_apply_reg to map your surface mask to fsaverage (make sure to --no-rev since you are mapping a mask). If you want to do FDR, then run mri_fdr.

On 1/29/18 12:17 PM, Charlotte Grosse Wiesmann wrote:

Dear freesurfer experts,

I would like to restrict my surface analyses (cortical thickness and surface area) to a mask from an fMRI meta-analysis using my own subject-specific template that I created with ANTS. So far, I have used Qdec and wanted to correct for cluster size running the Monte Carlo (MC) simulation on my own template. Now I would like to restrict the simulation to my mask to do a small volume correction in my regions of interest. I mapped the mask to my own template (in volume space) using ANTS (WarpImageMultiTransform) but how can I get this mask to the surface space to run the MC simulation on my own template within this mask?

I was planning to do: mri_mcsim --o my_template/mult-comp-cor/my_template/lh/mymask --base mc-z --surface my_template ?h --nreps 10000 --mask mymask.mgz

How do I get mymask.mgz in the correct space for this?

And can I continue using Qdec or do I have to use glmfit for these analyses?

In addition: is it also possible to do a small volume correction using FDR rather than cluster-size correction?

Thanks for your help!

Charlotte _______________________________________________ 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

_______________________________________________ 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

Hi Doug,

great, this works well, thank you very much!

Best

Charlotte

----- Original Message ----- From: "Douglas N. Greve" dgreve@mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 14, 2018 11:37:13 PM Subject: Re: [Freesurfer] mri_vol2surf - what register.dat file to use?

You should be able to use --regheader ANTSaverage (assuming ANTSaverage is the name you gave it when running recon-all)

On 03/12/2018 01:32 PM, Charlotte Grosse Wiesmann wrote:

Hi Doug,

I was trying to map my volume mask from my study-specific average subject template space to the surface (still in my average subject template space) with mri_vol2surf as you suggested below. How d I get the correct register.dat file do do this?

I have tried bbregister but am not sure what subject and what moveable volume I need to take since I am basically staying in the same space (my own average subject space).

I am stuck with my analysis on this and would highly appreciate your help!

Thank you very much in advance!

Charlotte

----- Original Message ----- From: "wiesmann" wiesmann@cbs.mpg.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Friday, February 9, 2018 7:45:35 PM Subject: Re: [Freesurfer] REPOST: mri_mcsim with mask - How do I map a volume mask to the surface space for mri_mcsim using my own template?

Hi Doug,

thank you very much for your help! I am sorry for the naive questions, but I am not very familiar with surface analyses: I ran recon-all on my template ("ANTSaverage") so that I have the surfaces. Is it correct that I have registered my volume mask to my template space before I map it onto the surface with mri_vol2surf? And where do I get the registration file from to run mri_vol2surf?

I am also not quite sure I understand why I have to register the surface mask to fsaverage then rather than to my own template?

I am sorry for these questions, but I am a bit confused and would really appreciate your help!

Charlotte

----- Original Message ----- From: "Douglas Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Saturday, February 3, 2018 8:58:49 PM Subject: Re: [Freesurfer] REPOST: mri_mcsim with mask - How do I map a volume mask to the surface space for mri_mcsim using my own template?

You need to map the mask into the fsaverage space. Probably the easiest way to do this is to run recon-all on your template to get surfaces. Then run mri_vol2surf to map your mask onto the surface, then use mris_apply_reg to map your surface mask to fsaverage (make sure to --no-rev since you are mapping a mask). If you want to do FDR, then run mri_fdr.

On 1/29/18 12:17 PM, Charlotte Grosse Wiesmann wrote:

...

Dear freesurfer experts,

I would like to restrict my surface analyses (cortical thickness and surface area) to a mask from an fMRI meta-analysis using my own subject-specific template that I created with ANTS. So far, I have used Qdec and wanted to correct for cluster size running the Monte Carlo (MC) simulation on my own template. Now I would like to restrict the simulation to my mask to do a small volume correction in my regions of interest. I mapped the mask to my own template (in volume space) using ANTS (WarpImageMultiTransform) but how can I get this mask to the surface space to run the MC simulation on my own template within this mask?

I was planning to do: mri_mcsim --o my_template/mult-comp-cor/my_template/lh/mymask --base mc-z --surface my_template ?h --nreps 10000 --mask mymask.mgz

How do I get mymask.mgz in the correct space for this?

And can I continue using Qdec or do I have to use glmfit for these analyses?

In addition: is it also possible to do a small volume correction using FDR rather than cluster-size correction?

Thanks for your help!

Charlotte _______________________________________________ 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

---

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

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