Re: [Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution Hi experts, I have extracted the area of the significant cluster with the command like the following: mri_segstats --i mgh/lh.volume.all.mgh --seg glmdir_az_vz/lh.volume.all.glmdir/av-group2-vs-group2/cache.th20.neg.sig.ocn.mgh --id 1 --sumwf

Re: [Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution Hi Douglas, You instruction works perfect. Thanks a lot. Regards, Ting > On Aug 14, 2018, at 11:01 AM, Ting Li wrote: > > Hi experts, > > I have a significant cortical thickness cluster and want the cluster > thickness information in every

Re: [Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution Dear Bruce and Doug, Thank you so much. Its working perfectly fine. Best, MJ On Tue, Aug 14, 2018 at 8:51 AM, Douglas Greve wrote: > First, run mris_preproc and mri_surf2surf commands as before to create a > stack of P2 and P3. If you ran

Re: [Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution Hi experts, How to create the stack of P2P3.stack.mgh after mris_preproc and mir_surf2surf? Great thanks. Regards, Ting > On Aug 14, 2018, at 10:51 AM, Douglas Greve wrote: > > First, run mris_preproc and mri_surf2surf commands as before to

Re: [Freesurfer] Using a cluster as an ROI for further analysis

First, run mris_preproc and mri_surf2surf commands as before to create a stack of P2 and P3. If you ran mri_glmfit-sim on P1,  then you will have an "ocn" output file. You can run mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf P2P3.means-in-clusterN.dat where N is the number of

Re: [Freesurfer] Using a cluster as an ROI for further analysis

Hi Martin create a label for X1, then use mri_label2label to map it to each of your subjects in P2 and P3 cheers Bruce On Mon, 13 Aug 2018, Martin Juneja wrote: External Email - Use Caution For instance, if there is any way to extract spatial location of cluster X1 and

Re: [Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution For instance, if there is any way to extract spatial location of cluster X1 and use this location to extract thickness values of all the subjects from P2 and P3, that way I can perform two-sample t-test. I am not sure if that's feasible and if so, then

[Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution Hi experts, I found a cluster X1, which showed significant difference in cortical thickness between two groups C1 and P1, determined using mris_preproc, mri_surf2surf and mri_glmfit commands. I am interested in determining if the same cluster X1 has