Re: [Freesurfer] Cannot load overlay through GUI

2020-02-04 Thread Fengdan Ye
External Email - Use Caution Hi Ruopeng, Thank you a lot for the response! This fixed my problem. Best, Fengdan > On Feb 4, 2020, at 12:20 PM, Ruopeng Wang wrote: > > Hi Fengdan, > > Can try the latest development build of freeview? It should work better > on newer macOS. Y

Re: [Freesurfer] Cannot load overlay through GUI

2020-02-04 Thread Ruopeng Wang
Hi Fengdan, Can try the latest development build of freeview? It should work better on newer macOS. You can get it from here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng On 1/29/20 5:20 PM, Fengdan Ye wrote: > External Email - Use Caution > > Dear FreeSurfer

Re: [Freesurfer] activation timeseries

2020-02-04 Thread Douglas N. Greve
Hi Mona, I'm not sure what you are trying to do here. Using a different program is not going to make your data less noisy. The mri_glmfit command will remove mean, etc, but you are running it on fmc.nii.gz which is in the native functional space. If this is what you want to do, then run it on f

Re: [Freesurfer] PetSurfer questions

2020-02-04 Thread Douglas N. Greve
On 2/3/2020 11:56 PM, Soo-Jong Kim wrote: External Email - Use Caution Thank you, Dr. Greve I checked all about your comment. I have questions more. 1. I found that volumes or counts in gtm.stats.dat are for native PET space. If co-registered PET onto corresponding MRI(i.e. MRI spa

Re: [Freesurfer] Highlighting single atlas structures in freeview

2020-02-04 Thread Francesco Puccettone
External Email - Use Caution Hello Andrew-or others who might wish to help :-] I've had to come back to this task after a while. I no longer have access to the Linux PC, thus will need to do this on my Windows 10 installation of FS (Oracle VM). What is the easiest way of achieving

[Freesurfer] activation timeseries

2020-02-04 Thread Nasiriavanaki, Zahra
Dear Freesurfer experts I want to extract "activation timeseries (BOLD signal changes in each time point) " from a predefined ROI in a single subject task fMRI data. Previously, I extracted these values from fmcpr.sm0.self.lh.nii.gz by using mri_segstats, but the data seems to be too noisy. I

Re: [Freesurfer] mri_deface error: could not find wm peak

2020-02-04 Thread Tim Schäfer
External Email - Use Caution Hi Bruce, I have uploaded an input file via FTP to /transfer/incoming/rawavg.mgz on ftp://surfer.nmr.mgh.harvard.edu. I am using FreeSurfer v6 stable under MacOS. The full command line (bash shell) is: cd path/to/rawavg.mgz mri_deface rawa