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" <wiesm...@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" <gr...@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
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