Re: [Freesurfer] kill recon-all programatically/remotely

ps aux | grep recon-all To get the pid, then kill -9 pid Or killall recon-all If it is the only one running on that box Cheers Bruce > On Mar 31, 2020, at 10:10 PM, Octavian Lie wrote: > >  > External Email - Use Caution > > Dear All, > > Is there a way to kill a

[Freesurfer] kill recon-all programatically/remotely

External Email - Use Caution Dear All, Is there a way to kill a recon-all run on linux via ssh/putty. Ctrl+C is not working, obviously, and it is not easy to figure out which process encodes the recon-all runs with commands such as ps aux, top etc. One gross way may be removing

Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

External Email - Use Caution Hello Tristan, Going back to that thread, I’d like to try the command you uploaded data for asfreesurfer_data.tar.gz on a couple of Ubuntu systems, but either I’m looking in the wrong place or it’s not there anymore. Is there a shared google drive

Re: [Freesurfer] Reducing FreeSurfer recon-all time

Hi Xiaojiang do you have multiple cores? If so, you can use -openmp 4 or something to reduce the recon time even on your linux box cheers Bruce On Tue, 31 Mar 2020, Xiaojiang Yang wrote: External Email - Use Caution Freesurfer experts: I know in my powerful Linux

[Freesurfer] Reducing FreeSurfer recon-all time

External Email - Use Caution Freesurfer experts: I know in my powerful Linux machine, recon-all needs about 10 hours to finish all computation. What is the possible way I can use to greatly reduce this computation time from 10 hours to, say 1-3 hours? Is Sun Grid Engine (SGE),

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

Uuuummm this is a tough one. Any ideas, Andrew? Maybe updating java? Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience"

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

External Email - Use Caution Hello Eugenio, No I wasn't! When I first tried to run the subfields I wasn't pointed to downloading a version of Java. I do have Java on the MAC I'm using, but the error "unable to start JVM because of a bad java option" still appears. Any other ideas

Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm

External Email - Use Caution Just to update, I found another version of mri_surfcluster that you (Doug) linked from the archives, with a build date of April 3, 2019, and that apparently worked just fine. I'm not sure where I got the one I downloaded. Sorry for the red

Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

External Email - Use Caution Thanks for the reply, all. The issues I'm having are the same as they were in my prior thread, found here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63458.html I tried everything up to and including compiling everything from

Re: [Freesurfer] Using freeview to view (and edit?) talairach registrations

You can go to menu Tools -> Transform Volume to adjust the registration and save it as a lta registration file. Then run lta_convert to convert it to xfm: lta_convert --inlta foo.lta --outmni foo.xfm > On Mar 31, 2020, at 1:06 PM, Rachel Hoel > wrote: > >

Re: [Freesurfer] Issue with tkregister command

I think this is a bug. Can you try this version? https://gate.nmr.mgh.harvard.edu/safelinks/greve/reg-feat2anat copy it to $FREESURFER_HOME/bin and run chmod a+x $FREESURFER_HOME/bin/reg-feat2anat On 3/31/2020 11:46 AM, Tiffany Bell wrote: External Email - Use Caution Hello I am

[Freesurfer] Issue with tkregister command

External Email - Use Caution Hello I am trying to transform a free surfer segmentation to functional space using reg-feat2anat but I get the error tkregister2_cmdl_cmdl: Command not found. I am running freesufer on linux through a virtual machine. See below for the full

Re: [Freesurfer] Using freeview to view (and edit?) talairach registrations

Hi Rachel, You need to enter the full path of the transformation file or relative one like /mri/... Best, Ruopeng > On Mar 31, 2020, at 12:20 AM, Rachel Hoel wrote: > > External Email - Use Caution > Dear Freesurfer Developers, > > I'm working with v6.0 on OS Catalina 10.15

Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

External Email - Use Caution We would also like to know about any issues you are seeing on Ubuntu.. I think Ubuntu eliminated some jpeg/png packages from their repos. Those can be downloaded and installed manually,e.g., libpng12-0_1.2.54-1ubuntu1.1_amd64.deb,

Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8

External Email - Use Caution Hi Tristan, I'm about to setup a FreeSurfer installation on an Ubuntu system, and I wondered whether you could elaborate on the kind of issues you are experiencing. Best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of