[Freesurfer] Project volumes in MNI to lrsym_fsaverage6

Dear freesurfer experts I have processed resting state fMRI data in MNI space , for example: Data: 91*109*91*240, 240 was the time frames number. How could i project the data in MNI space to the symmetric surface(eg lrsym_fsaverage6) ? Thanks in advance! Meiling

[Freesurfer] Project volumes in MNI to lrsym_fsaverage6

Dear freesurfer experts I have processed resting state fMRI data in MNI space , for example: Data: 91*109*91*240, 240 was the time frames number. How could i project the data in MNI space to the symmetric surface(eg lrsym_fsaverage6) ? Thanks in advance! Meiling __

[Freesurfer] create symmetric mask on surface

Dear freesurfer experts I created a binary mask on fsaverage4(eg: lh.mask.fs4.mgh) with 30 vertices included in the mask on the left hemisphere, how can i obtain a symmetric mask on the right hemisphere that covered the same regions like the mask on the left hemisphere? Thanks! Meiling __

[Freesurfer] How to divide the lateral and medial vertex index of fsaverage4?

Dear Freesurfer Now I have two ROIs on the fsaverage4, one on the lateral and the other is the on the medial, how can i separate apart the two rois? Acutally, how can i divide the vertex index of the lateral and medial on fsaverage4 or fsaverage5? Thanks in advance! Meiling

[Freesurfer] GRF correction in mri_glmfit-sim

Dear FS experts I do GRF correction using mri_glmfit-sim --grf in volume. I find --grf pos and --grf neg, but not --grf abs. My first question is, is the --grf just used for ONE-side correction? For instance, we can test, are the FCs of patients larger than that of healthy controls or smaller

[Freesurfer] FDR cluster-level Correction

Hi Freesurfer experts I am doing FS-nonlinear volume based FC analysis with cluster-level correction. 1. Could you please point me which command can do the FDR cluster-level Correction? 2. If i do correction using MonteCalo cluster-based correction. Is it right like the following command mri_gl

[Freesurfer] FDR clustr-level Correction

Hi Freesurfer experts I am doing FS-nonlinear volume based FC analysis with cluster-level correction. 1. Could you please point me which command can do the FDR cluster-level Correction? 2. If i do correction using MonteCalo cluster-based correction. Is it right like the following command mri_gl

[Freesurfer] cluster_wise correction

Hello Freesurfer Experts I am emailing to ask aome questions about cluster_wise correction on surf. I hope some experts here could help me... The seed_based functional connectivity maps are generated in two groups, such as Patient and HC. I do the functional connectivity comparison between the tw

[Freesurfer] cluster_wise correction

Hello Freesurfer Experts I have got the statistic P map ( -log10(p)),such as the 'Patient-smaller-Control_P_on_fsaverage4_lh.mgh', now i want to do the cluster_wise correction with p<0.05., or do the FDR correction. Could you please give me some suggestions how to do it? Thank you very much!

[Freesurfer] how to do surface cluster-wise correction and how to judge the adjacent vertices of a specified vertex

Hello Freesurfer experts Now i got the task activation on fsaverage4 template, but still so many vertices are isolated after a threshold was set (such as Z>1.96). I want to keep the vertices which become clusters although they have small Z values. It looks like mri_surfcluster can achieve my

[Freesurfer] how to judge a set of continuous vertices in fs4 template

Dear freesurfer Now i got the task activation on fsaverage4 template, but still so many vertices are isolated after a threshold was set (such as Z>1.96), how can i remove the vertices if there are less 5 continuous vertices next to them? And how can i calculate the first order difference of the

[Freesurfer] Convert volume index to vertex number in surface

hello I have some points defined in volume (RAS coordination) and now I want to see these locations (vertex number) on surface. I don't know how to do it. I can see one point using tkmedit, input the coordination and save point and then in tksurfer, go to saved point, so I can get the vertex num

[Freesurfer] help-convert vome index to vertex numbe in surface

hello I have some points defined in volume (RAS coordination) and now I want to see these locations (vertex number) on surface. I don't know how to do it. I can see one point using tkmedit, input the coordination and save point and then in tksurfer, go to saved point, so I can get the vertex num