Re: [Freesurfer] FreeSurfer LocalGI error

2018-01-16 Thread Manoj Kumar
Thank you very much, Dear Andrew! for your expert advise. I really appreciated. Its worked. Best Regards Manoj On Tue, Jan 16, 2018 at 10:39 PM, Hoopes, Andrew wrote: > Hi Manoj, > > This probably has to do with SIP being enabled, which blocks libraries > stored in /usr. I would suggest disabli

[Freesurfer] POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING

2018-01-16 Thread Xiaosong He
*POST-DOCTORAL FELLOWSHIP* *IN NEUROIMAGING * *THOMAS JEFFERSON UNIVERSITY/ SIDNEY KIMMEL * *MEDICAL** COLLEGE, PHILA., PA.* The Department of Neurology at Thomas Jefferson University/Jefferson Medical College has an opening for a Two-Year Postdoctoral Research Fellowship in Neuroimaging focusi

Re: [Freesurfer] Longitudinal Pipeline (fwd)

2018-01-16 Thread Aaron Tanenbaum
Oh wow. thank you very much. You just save me weeks worth of work. On Tue, Jan 16, 2018 at 2:31 PM, Bruce Fischl wrote: > FYI > > -- Forwarded message -- > Date: Tue, 16 Jan 2018 19:59:38 + > From: Mark Jenkinson > To: Bruce Fischl > Cc: Freesurfer support list > Subject:

[Freesurfer] Research Assistant Positions in ECoG Lab in New York

2018-01-16 Thread steph
Dear all, The ECoG Laboratory for Human Brain Mapping at the Feinstein Institute for Medical Research – Hofstra Northwell School of Medicine is looking for two research assistants. The successful candidates will help with the lab’s research into (1) improving the identification of functional

Re: [Freesurfer] Longitudinal Pipeline (fwd)

2018-01-16 Thread Bruce Fischl
FYI -- Forwarded message -- Date: Tue, 16 Jan 2018 19:59:38 + From: Mark Jenkinson To: Bruce Fischl Cc: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal Pipeline Hi Aaron and Hi Bruce! There is code to convert ANTs format to FSL, so you can use that. It is pa

Re: [Freesurfer] recon-all exited with error

2018-01-16 Thread Bruce Fischl
you can put it on our ftp site: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote: > Hi Bruce > Thanks for the speedy reply. Should I attach it here or is there a place I > can upload it to? > > best > Trisanna > > -- > Ph.D. CandidateM

Re: [Freesurfer] FreeSurfer LocalGI error

2018-01-16 Thread Hoopes, Andrew
Hi Manoj, This probably has to do with SIP being enabled, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best, Andrew On Jan 16, 2018, at 2:59

Re: [Freesurfer] Cortical White matter/corpus callisum

2018-01-16 Thread Del Re, Elisabetta
Alan, thank you. Of course, but my question was different: Is the volume of the corpus callosum included in the calculation of the volume of the 'cerebral white matter'? Or does the volume of the cerebral white matter not include the volume of the corpus? My understanding is that the volume o

Re: [Freesurfer] recon-all exited with error

2018-01-16 Thread Trisanna Sprung-Much
Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a place I can upload it to? best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl wrote: > hmmm, I've never seen label2label cor

Re: [Freesurfer] recon-all exited with error

2018-01-16 Thread Bruce Fischl
hmmm, I've never seen label2label core dump before. Can you tar, gzip and upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote: > Hi there > > I ran Freesurfer 6.0 on a subject last night and it took about 12 hours > (seemed to get to the very end) and then exited wit

Re: [Freesurfer] Cortical White matter/corpus callisum

2018-01-16 Thread Alan Francis
Hello Elisabetta - The Corpus callosal volumes are included in the ASEG output and not in the WM files. They are titled CC_Anterior, CC_Midbody etc. Best, Alan On Mon, Jan 15, 2018 at 2:11 PM, Del Re, Elisabetta < elisabetta_de...@hms.harvard.edu> wrote: > Dear experts, > Is the corpus callosu

[Freesurfer] PhD and postdoctoral positions - Investigating sensory aspects of human communication

2018-01-16 Thread Katharina von Kriegstein
Several researcher positions (Postdocs and PhD students) are available at the Human Communication Research Group, led by Katharina von Kriegstein. The group is currently based at the Max Planck Institute for Human Cognitive and Brain Sciences in Leipzig (MPI CBS; http://www.cbs.mpg.de/independe

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

2018-01-16 Thread Martin Reuter
Hi Lanbo, what is the exact command you use for this? The problem is that the script or your command does not pass the right flags to recon all. Whenever recon-all is supposed to work on a longitudinal directory it needs to know the base and the long so the recon all command needs to show -l

[Freesurfer] FreeSurfer LocalGI error

2018-01-16 Thread Manoj Kumar
Hello Dear FreeSurfer Experts, I am trying to run "recon-all -s subject -localGI" command on my Mac bash terminal. I am getting following error. I am using using Freesurfer V 6.0 and running on MacOS High Sierra (version 10.13) I also run the istallation update :"sudo -E fs_update" as per su