[Freesurfer] Errors on compiling FreeSurfer

Hi Experts, I tried to compile FreeSurfer on Ubuntu 16. When I ran a command 'make check', I got these error messages: */usr/bin/ld: warning: libtk8.4.so , needed by /home/aziz/centos6-x86_64-packages/KWWidgets/current/lib/KWWidgets/libKWWidgets.so, not found (try using

[Freesurfer] Build Freeview on macOS

Hi Freesurfer experts, Based on this link https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page, it mentions that "*As of the writing of this document (June 2016) freeview is unable to build on macOS 10.11 platforms and higher (El Capitan and higher)." * Could we build

[Freesurfer] Compile problems

Hi Freesurfer experts, I ran the commands to build Freesurfer (Yosemite based) by following this link https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page However, I got the error message when I ran *`make install'* command as follows: gunzip: can't stat:

[Freesurfer] Error when trying to compile the code

Dear FreeSurfer Experts, I was trying to compile the FreeSurfer code by following steps shown in https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page However, I got this error message after I ran ./configure configure: error: FATAL: netcdf lib not found. Set LDFLAGS or

[Freesurfer] Freesurfer commands

Hi Freesurfer Experts, Currently, I am using these command excited in Matlab to extract the coordinates of volume. *mri = MRIread('aseg.mgz');pos = find(mri.vol == 17 | mri.vol == 53);* *[i,j,k] = ind2sub(mri.volsize,pos);* I would like to run these command in the Freesurfer itself rather than

Re: [Freesurfer] Specification of computer

, 2017 at 9:46 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > yes it does, and it should significantly reduce execution time unless you > don't have multiple cores > > cheers > Bruce > > On Sat, 4 Feb 2017, Aziz Nanthaamornphong wrote: > > Hi Bruce, >>

Re: [Freesurfer] Specification of computer

course you can specify -openmp 8 for exmaple to use 8 cores, > which speeds things up a lot. It also depends how many recons you will be > running at the same time. A 16 core machine with 64G of ram would be able > to run 4 recons in a few hours each. > > cheers > Bruce > > >

[Freesurfer] Specification of computer

Hi experts, I would like to find a new high-performance computer to run the reconstruction process in Freesurfer. Currently, I used a single computer (Intel core i7, RAM 8MB) to run the commands (e.g., 'recon-all -all' ) that spent average time 7-9 hours per one subject data. Please let me know

Re: [Freesurfer] Freesurfer 6.0 link

Thank a lot. Aziz. On Wed, Jan 25, 2017 at 9:38 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall > > On 01/25/2017 05:44 AM, Aziz Nanthaamornphong wrote: > > Hi experts, > > > > How can

[Freesurfer] Freesurfer 6.0 link

Hi experts, How can I download Freesurfer version 6.0? Is there an available URL link? Thank you, Aziz -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket

Re: [Freesurfer] Cannot allocate memory error

view -f $SUBJECTS_DIR//surf/lh.inflated.nofix > > > > cheers > Bruce > > > On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: > > Hi Bruce, >> How can I look at inflated.nofix as you mentioned? I think I ran recon-all >> for the 001.mgz without other files. >

Re: [Freesurfer] Cannot allocate memory error

tains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -

[Freesurfer] Cannot allocate memory error

Hi experts, I ran the command $recon-all -all -subjid 0696 I have got these error messages *CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)* *Excessive topologic defect encountered: could not allocate 322592700 edges for retessellation* *Cannot allocate memory* *Linux

Re: [Freesurfer] Coordinates of particular volumes

, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Aziz, > > make sure $FREESURFER_HOME/matlab is in your matlab path. > > cheers > Bruce > > On Mon, 12 Sep 2016, Aziz Nanthaamornphong wrote: > > >> Which the version of Matlab has a 'MRIread' fun

Re: [Freesurfer] Coordinates of particular volumes

gt; cheers > Bruce > > > On Sun, 4 Sep 2016, Ruyuan Zhang wrote: > > >> Hi, Aziz >> >> You can use MRIread function to read in a volume (i.e. >> brainmask.mgz). >> You will get a structure, which contains a field called ras2vox. >> >> c

Re: [Freesurfer] Coordinates of particular volumes

t; > can you elaborate? What coordinates do you want? What are you trying to do > with them? The .mgz format contains ras2vox matrices that let you go from > voxel indices to RAS coordinates and such. > > > cheers > Bruce > > > On Sun, 4 Sep 2016, Aziz Nanthaamornpho

[Freesurfer] Coordinates of particular volumes

Dear Freesurfer experts, How can we get the coordinates (X, Y, Z) of a particular volume? I couldn't find any functions or command to do that. Thank you in advance. Aziz. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] All coordinates of volume of interest

Hi, Is there a way to get all coordinates (x,y,z) of the particular volume of interest (e.g., left-insula, left-thalamus)? Best, Aziz. -- Aziz Nanthaamornphong, Ph.D., Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http

[Freesurfer] Compile and Install on El Capitan

Hi, Can we compile & install Freesurfer on El Capitan? Unfortunately, I found the document for Lion ( https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page). Thank you, Aziz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu