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: email@example.com 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