Re: [Freesurfer] Third party dependencies directory not found when building from source

External Email - Use Caution ​Hello Christian, Allow me to suggest that you try following the instructions for the Fresrufer cmake build located here, http://freesurfer.net/fswiki/CMake Besides the option to build the 3rd party packages with build_packages.py script, you can also

Re: [Freesurfer] Segmentation of thalamic nuclei - no reticular nucleus

External Email - Use Caution Hi HSK We use it in the model fitting but do not segment it due to the absolute lack of contrast with the white matter. Kind regards, Eugenio -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedic

[Freesurfer] Third party dependencies directory not found when building from source

External Email - Use Caution Hello Developers, I am attempting to build Freesurfer from source on my Ubuntu 18.04.1 LTS machine. I have followed the instructions on the freesurfer_linux_developers wiki, and have suc

[Freesurfer] Pediatric longitudinal pipeline

Hi all, We are looking at analyzing cortical thickness across time in a group of children. Ages are 6-16 and children each have one followup visit, between 1-3 years from first visit. We first ran the cross-sectional pipeline and analyzed change that way before coming across the longitudinal p

Re: [Freesurfer] Getting the volume of a ?h.pial-outer-smoothed file

External Email - Use Caution Hello Bruce, I believe the mris_volume program / command is exactly what I was looking for. Thanks a bunch! Best, Riccardo On Tue, Oct 30, 2018 at 3:57 PM Bruce Fischl wrote: > Hi Riccardo > > when you say "compute the volume", what exactly do you

Re: [Freesurfer] Segmentation fault

External Email - Use Caution ​Hello Jon, Since trac-all is a tcsh script, you could try prefacing it with "tcsh -x" to get extra output about what it is doing, i.e., $ tcsh -x trac-all  rest of args... - and then look thru the trac-all output to see where it actually runs a bi

Re: [Freesurfer] Getting the volume of a ?h.pial-outer-smoothed file

Hi Riccardo when you say "compute the volume", what exactly do you mean? If you want the interior volume of the two surfaces, you can use mris_volume, which uses the divergance formula to do the calculation cheers Bruce On Tue, 30 Oct 2018, Riccardo Falsini wrote: External Email

[Freesurfer] Getting the volume of a ?h.pial-outer-smoothed file

External Email - Use Caution Dear Freesurfer experts, Hello, I am a student currently working in Frank Guenther's lab at Boston University. I am quite new to freesurfer, so forgive me if the following question may be elementary. I am interested in using freesurfer to compare the

[Freesurfer] Segmentation of thalamic nuclei - no reticular nucleus

External Email - Use Caution Dear all, I ran thalamic nuclei segmentation tool using the "freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa" version. The segmented thalamic nuclei were visualized well by FreeView and were able to find most nuclei. But there is no reticular n

Re: [Freesurfer] Matlab Segmentation error when running hippocampal segmentation in dev version

External Email - Use Caution Hi Jaime, Can you please send us the output you get between calling the command and the error? Cheers, /E -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College Lo

Re: [Freesurfer] segmentHA_T1 error DYLD_LIBRARY_PATH

External Email - Use Caution It seems it could be a version conflict. Please try unsetting DYLD_LIBRARY_PATH. Cheers, /Eugenio -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http

[Freesurfer] Postdoctoral position, University of Oslo (UiO)

External Email - Use Caution I am delighted to advertise the following postdoctoral position on behalf of Prof Anders M Fjell: At the Center for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have an available postdoc position for an excellent candidate,

[Freesurfer] Matlab Segmentation error when running hippocampal segmentation in dev version

External Email - Use Caution Hi, I think I have the same or similar error than [Freesurfer] error in hippocampal subfields and nuclei of amygdala segmentation I am running segmentHA_T1.sh for one subject an

[Freesurfer] segmentHA_T1 error DYLD_LIBRARY_PATH

External Email - Use Caution Hi, I have this error when I try to run segmentHA_T1.sh It seems that it sets up the wrong DYLD_LIBRARY_PATH, the one I have in my bash_profile is /Applications/MATLAB_R2016a.app/bin/maci64:/Applications/MATLAB_R2016a.app/sys/os/maci64:/Applications/MA

Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}

External Email - Use Caution Hi Martin, That was helpful! Thanks a lot =)! Sincerely, Guoyang From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Tuesday, 30 October, 2018 3:42 PM To: Freesu

Re: [Freesurfer] error in hippocampal subfields and nuclei of amygdala segmentation

External Email - Use Caution Dear Eugenio I have 8GB 2400 MHz DDR4. I am not sure this might be a problem cause now I run only freesurfer to segment hippocampal subfields and nuclei of amygdala with mac. I already updated the freesurfer to the latest version and installed matlab r

Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}

External Email - Use Caution Hi Gouyang There's no T2 longitudinal pipeline available at the moment. In its absence, what you're doing is the way to go ;-) Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvar

Re: [Freesurfer] error in hippocampal subfields and nuclei of amygdala segmentation

External Email - Use Caution Dear J How much RAM memory do you have? Andrew: do you think this might be the problem? Cheers E Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 오진영 Se