[Freesurfer] Fwd: Overall maxima is high and still no significant cluster

2018-12-05 Thread Martin Juneja
External Email - Use Caution Dear experts, Could you please help me in resolving following issue? Thanks. -- Forwarded message - From: Martin Juneja Date: Wed, Nov 28, 2018 at 2:23 PM Subject: Overall maxima is high and still no significant cluster To:

Re: [Freesurfer] Freeview command not found {Disarmed}

2018-12-05 Thread fsbuild
External Email - Use Caution It should be OK to use qt4 on Ubuntu 16, though I think qt5 would work as well. Please test to see if you can freeview from where it was installed. Your output below says that FREESURFER_HOME is /usr/local/freesurfer, so you should have a

Re: [Freesurfer] Freeview command not found

2018-12-05 Thread Maeve Barrett
External Email - Use Caution *Thanks so much!* *I installed the qt4 library but I received another error the* 'freeview: command not found error' *When I attempted it again, I received the following error:* freeview.bin $argv freeview.bin: error while loading shared libraries:

Re: [Freesurfer] Freeview command not found

2018-12-05 Thread fsbuild
External Email - Use Caution Hello Maeve, You can search for the package to install with apt-file, but you may need to install that first, so try, $ sudo apt install apt-file $ sudo apt update … now search for the package with that library name using apt-file $ sudo apt-file

Re: [Freesurfer] mris_preproc paired diff outputs 0 values

2018-12-05 Thread Sims, Sara A
External Email - Use Caution I have now gotten this to run on 3 subjects. However I have 786 subjects and need to find the bad apple. Is there a way I can do quality checks on each subject’s difference map in fsaverage space that mris_preproc has made? Basically I want to cycle

[Freesurfer] Freeview command not found

2018-12-05 Thread Maeve Barrett
External Email - Use Caution *Hello,* *I've been trying to resolve this issue but I haven't found a fix on the mailing lists. I downloaded and installed the most recent version of Freesurfer for Linux. I am running Ubuntu 16.04 LTS as guest on Virtualbox 5.2.22 on a windows 10

[Freesurfer] Lab manager position in Perception & Brain Dynamics Laboratory at NYU Medical Center

2018-12-05 Thread Max Levinson
External Email - Use Caution The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at Langone Medical Center, New York University is looking for a lab manager to start in summer 2019. The Laboratory is within the Neuroscience Institute at NYU Langone Health

[Freesurfer] hippocampus cortex surface

2018-12-05 Thread Yixin Ma
External Email - Use Caution Hi Freesurfer experts, After running the segmentation of hippocampus subfields, I'm wondering if I can get the surface of the gray matter and white matter of hippocampus in addition to subfields. My goal is to divide the hippocampus cortex into

Re: [Freesurfer] Registering Anatomical Parcellation to DWI

2018-12-05 Thread Yendiki, Anastasia
Yes, you can register other modalities to the T1 using bbregister. Then you can use that registration to transform any volume from T1 space to the space of the other modality. Check out the multimodal integration tutorials on the freesurfer wiki. On Dec 5, 2018 2:36 AM, Maedeh Khalilian

Re: [Freesurfer] Map image in MNI onto fsaverage

2018-12-05 Thread Thomas Yeo
External Email - Use Caution Hi John, Not sure if you still need this, but you can use our approach instead: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion Regards, Thomas On Tue, Nov 20, 2018 at 2:15 AM john Anderson

[Freesurfer] Outer smoothed surface (lh.pial-outer-smoothed) only partly 'real' outer surface

2018-12-05 Thread M. Jordan
External Email - Use Caution Hi!, i am using recon-all -s -localGI to get the outer smoothed surface of the pial files. This works, but when loading the original pial and the smoothed one, some parts of the original pial stand out. Is there any possibility / parameter to avoid