[Freesurfer] mri_label2vol in matlab

Hi Freesurfer experts, I have a label with 1500+ vertices I'd like to convert to a nifti file. Right now I use mri_label2vol and output a file I'd like to do this in matlab, is there any way? More specifically, I'd like to get the native co-ordinate for each vertex in the nifti file. The vox2ras co

Re: [Freesurfer] 2D sphere co-ordinates

That worked perfectly! Thanks ___ 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 beli

Re: [Freesurfer] 2D sphere co-ordinates

Hi Bruce, That sounds great! Can you refer me to a wiki page that shows how to do it? Or better yet, a matlab/bash script? Thanks! Jonathan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu

[Freesurfer] 2D sphere co-ordinates

Hi Freesurfer Experts! I'm looking to find the 2D co-ordinates for a vertex in the fsaverage surface I can find their 3D volume co-ordinates using read_surf but I'd like the 2D coordinates. I'll explain: I would like to study properties of the inflated STS. For each of the vertices I can find the 3

Re: [Freesurfer] Timecourses In freesurfer

Hi, In tksurfer I would like to be able to see the timecourse (Percent Signal Change) for a vertice or cluster of vertices I try to load a timecourse using file -> open timecourse and I cant find any file that will load Thanks! Jonathan ___ Freesurfer

Re: [Freesurfer] Timecourses In freesurfer

Hi Doug, I think I've realized what the problem is - my cespct file has only one frame How can I run mkanalysis-sess, mkcontrast-sess and selxavg3-sess in a way that produces the whole percent signal change time course? Thanks Jonathan ___ Freesurfer mail

Re: [Freesurfer] Timecourses In freesurfer

Hi Doug, My goal is to write a script in tcl using tksurfer that extracts the timecourse for each condition of my exp for my selected vertices. The problem is that there is no timecourse data when opening tksurfer and I can't find any file to load! My workflow is : recon-all for the anatomical scan

[Freesurfer] Timecourses In freesurfer

Hi All, I’ve been trying to get time course data in tksurfer I’ve used selxavg2 to create bfloat mgh and nii.gz files and yet I can’t load these into tksurfer! I must be missing something very basic - how do I generate a time course in free surfer? All I see is the f, beta and other single value

[Freesurfer] tksurfer batch mode without GUI

Hi experts, I've created many batch files that I would like to run in parallel using tksurfer -tcl scriptname.tcl Is there a way to ask tksurfer to run the script and process the graphical information (i.e. output tiff files I render using the tcl script) without physically showing the graphic

[Freesurfer] Single Subject Time Course

Hi all, I have analyzed several subjects ( recon-all, dcmunpack, preproc-sess, mkanalysis-sess, mkcontrast-sess, selxavg3-sess) and can see the contrast in tksurfer-sess and it all looks great! The problem is when I try to see the time course for a voxel/ROI the view -> windows -> time course graph