Re: [Freesurfer] Qdec not running ("image not found" error message)

External Email - Use Caution Hello Alex, It looks like you need to install Xquartz on your Mac with the X Windows libraries including libGLU.1.dylib. Download from here, open and run the installer package. https://www.xquartz.org/ - R. On Feb 25, 2020, at 23:27, Lab of Autism and

[Freesurfer] Qdec not running ("image not found" error message)

External Email - Use Caution Dear Freesurfer experts, Please help me with this simple error for running Qdec: - First I try to open qdec: qdec & - Then this occurs: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/qdec.bin Reaso

[Freesurfer] why topology fix almost takes 4 days to finish job

External Email - Use Caution Hello freesurfer experts I am using freesurfer to run recon-all, recon-all -i T1_MPRAGE image -t2 T2-FLAIR-ImageIt takes about 5 days to finish the process. I find that the most time consuming process is topology fix, it almost takes 4 days f

[Freesurfer] seg.mgz testing for FS7 beta

Hi Freesurfer team, I've run samseg for one participant, using the /mri/T1.mgz as the input, but the output seg.mgz is awful, w/ the ventricles being overestimated and the outer perimeter of the gray matter considered as the "Head-ExtraCerebral." I know in mind you all just want to know if it

[Freesurfer] beta testing FreeSurfer v7 beta: recon-all-status.log, samseg

External Email - Use Caution Dear experts, I began to test beta v7 version of FreeSurfer. I noticed that some entries in recon-all-status.log seem missing (i.e. white and pial surface placement - there is entry Cortical Parc while following entry is Refine Pial Surfs). Runn

[Freesurfer] Read Freesurfer surfaces and annotation files in C++

External Email - Use Caution Hi, there are some easy to use Matlab/Python functions to read/write native Freesurfer files (.annot, surfaces etc.) available. Anyone knows something similar for C++ (VTK)? Thank you. ___ Freesurfer mailing

[Freesurfer] Question about skull strip error

External Email - Use Caution Dear Freesurfer expert, I ran recon-all on one subject and part of the cortex was excluded. I followed the FS tutorial to change the watershed preflooding height percentage by using the command below: recon-all -skullstrip -wsthresh 30 -clea

[Freesurfer] lme models time or time^2

External Email - Use Caution Dear FreeSurfer expert I have a lme model with 3 timelines where one timeline is baseline. I two models y = intercept + time + group + sex + time_at_baseline and y = intercept +time +time² + group + sex +time_at_baseline Both time² and time is

Re: [Freesurfer] Cannot allocate memory

Hi Gabriel they are in the subject's directory. Have you gone through the FS tutorials on our wiki? That would be a good place to start cheers Bruce On Tue, 25 Feb 2020, Gabriel Tapia wrote: External Email - Use Caution Hello Bruce thank you for your quick reply, Where shou

Re: [Freesurfer] DOSS questions

External Email - Use Caution Thank you so much for all the help! Below you can find few remaining questions I have following your suggestions! Message: 6 Date: Mon, 24 Feb 2020 09:24:00 -0500 From: "Douglas N. Greve" mailto:dgr...@mgh.harvard.edu>> Subject: Re: [Freesurfer] GLM D

Re: [Freesurfer] Cannot allocate memory

External Email - Use Caution They are all in the output folder of the subject. The noxfix files are surfaces (in /surf/), the mgz file is a volume (in /mri/). Tim > On February 25, 2020 at 4:24 AM Gabriel Tapia wrote: > > > External Email - Use Caution > > H