Re: [Freesurfer] Error running "Test your FreeSurfer Installation"

External Email - Use Caution Dear Rafael, I use Ubuntu 18.04, and installing libpng12 resolved the problem for freeview. Copy and paste the below to your terminal and you will be able to run freeview. - curl -O http://security.ubuntu.com/ubuntu/pool/main/libp/libpng /libpng12

Re: [Freesurfer] Error running "Test your FreeSurfer Installation"

External Email - Use Caution When I changed the permissions on the directory where FreeSurfer was installed and ran it from there, and all went well. However, when I tried to display the results with Freeview, there was a problem:error while loading shared libraries: libpng12.

[Freesurfer] hardware upgrade affect Freesurfer?

External Email - Use Caution Hi FreeSurfer Experts, Would upgrading computer hardware affect FreeSurfer output? We are using FreeSurfer version 5.3-HCP and we are considering upgrading our server. It will have the same operating system but different computer specs (memory, cpu

Re: [Freesurfer] Error running "Test your FreeSurfer Installation"

Hi Rafael, Is your subject directory stored on an external drive like an SD card? The “Function not implemented” error implies that symlinks are not supported on the filesystem that you’re saving to. Ubuntu 18 definitely supports symlinks and I see that SUBJECTS_DIR points to /media/rafa…. You

Re: [Freesurfer] Thickness problem

sig = -log10(p)*sign(contrast), so if p=.01, then sig=2. The sign(contrast) is the direction of the contrast On 12/19/2019 4:14 PM, Gwang-Won Kim wrote: External Email - Use Caution Hi Dr. Greve, Thank you for your comment. I compared cortical thickness bewteen two groups. I have a que

Re: [Freesurfer] Manual segmentation to volume

Use $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz as the target when you are using the 1mm (there is a mri2.mm folder for 2mm) On 12/19/2019 11:34 AM, Benjamin Ineichen wrote: External Email - Use Caution Many thanks for your quick reply! I tried your suggestion. I got the error fst

Re: [Freesurfer] Creating a label from overlapping cluster results

There is a script called labels_intersect. I have not run it before, but the name would indicate that it would do the right thing On 12/19/2019 9:49 AM, Bruce Fischl wrote: Hi Cody not sure we have a binary for this, but it would be about 5 lines of matlab code cheers Bruce On Thu, 19 Dec 2019,

[Freesurfer] Unable to run recon all

External Email - Use Caution Hello FS experts, I am trying to run recon all on about 100 subjects. But one out of 100 subjects finishes recon all with error, and doesn't complete the process. Here I am attaching recon all log for your reference. Also, before installing freesurfer

[Freesurfer] Fill holes in BOLD surface

External Email - Use Caution Hi Freesurfer experts, I have projected 4D-preprocessed BOLD data to Freesurfer cortical surfaces. Resulting individual surfaces have many holes (see attached image) that I would like to fill with nearest neighbors values around each hole (avoiding the

Re: [Freesurfer] mapping the reliability of separating GM/WM

sure, you should be able to make vertex-wise maps. I think Doug wrote something to do this, but if not I can modify mri_cnr to output mean and variance maps for gray and white easily enough. cheers Bruce On Fri, 20 Dec 2019, Liu Y wrote: External Email - Use Caution Hi Bru

[Freesurfer] matlab output issue

External Email - Use Caution > Hello FreeSurfer Developers, > > I'm helping researchers test Freesurfer 4.5 getting a Matlab error. I'm > wondering if this is a Freesurfer or Matlab issue. Any ideas? THANKS IN > ADVANCE. > > 1) FreeSurfer version: freesurfer-Linux-centos4_x86_