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" <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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