[Freesurfer] HIPS unsupported

Hallo, I have finished my test runs and have observed that using export DIAG=0x and export DIAG_VERBOSE=1 cause all recon-all runs to fail with the following error: HIPS unsupported No such file or directory I have tested different computing environments (container, hardware, VMs) using

[Freesurfer] methodological questions for manuscript

Hi! For my manuscript, the journal wants me to answer some questions on the methods that I used and I want to make sure I am giving correct information on how FreeSurfer calculates hippocampal volumes. Would it be possible to check my 4 answers and let me know if these are accurate? Question:

Re: [Freesurfer] -openmp flag in mri_em_register

yes, i'm using bash and it worked with export, thanks! On 8 June 2017 at 17:42, Bruce Fischl wrote: > what shell are you using? THat is a tcsh/csh command.If you are using bash > you need to use the export command > > cheers > Bruce > On Thu, 8 Jun 2017, Lisa Kramarenko wrote: > > Hi,thanks for

[Freesurfer] testing FS installation - apparent cursor RAS coordinate mismatch?

Hello, I just installed FS 6 (mac OS) and followed Examples 1, 2, 3 and 4 under the "Test your FreeSurfer Installation" section here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall I am getting a very different view of bert's brain when the cursor RAS coordinates are made to coincid

Re: [Freesurfer] Cortical thickness_Group analysis

Dear Douglas, Can I check with you if you have received my reply below to your question?? Thanks, Ali On Mon, Jun 5, 2017 at 10:16 PM Ali Radaideh wrote: > Thanks alot. > > Below are the commands I used in order: > > mris_preproc --fsgd disease_Healthy_Age.fsgd --target fsaverage --hemi lh >

Re: [Freesurfer] TRACULA -path issue

Hi Anastasia, thanks for your help but I actually did some independent digging and found that the problem seem to be an issue with memory allocation limits for the first step of TRACULA, causing that last step not to run. Although, I’m not sure if that problem is really it since I tried running

Re: [Freesurfer] -openmp flag in mri_em_register

what shell are you using? THat is a tcsh/csh command.If you are using bash you need to use the export command cheers Bruce On Thu, 8 Jun 2017, Lisa Kramarenko wrote: Hi,thanks for the quick reply. I pasted this line in the script, yet it gives me the following error: setenv: command not fou

Re: [Freesurfer] FW: Freeview Application

Recently Microsoft announced bash on Windows and initial tests within our group have shown that freesurfer and freeview work in this environment: https://msdn.microsoft.com/en-us/commandline/wsl/about However, currently freeview is not shipped as a separate stand-alone package from freesurfer.

Re: [Freesurfer] -openmp flag in mri_em_register

thanks a lot, now it works! On 8 June 2017 at 16:29, Harms, Michael wrote: > > The HCP Pipeline scripts use ‘bash’. (setenv is for the csh shell). > The equivalent for bash is: > > export OMP_NUM_THREADS=2 > > -- > Michael Harms, Ph.D. > -

Re: [Freesurfer] -openmp flag in mri_em_register

The HCP Pipeline scripts use ‘bash’. (setenv is for the csh shell). The equivalent for bash is: export OMP_NUM_THREADS=2 -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medi

Re: [Freesurfer] -openmp flag in mri_em_register

Hi, thanks for the quick reply. I pasted this line in the script, yet it gives me the following error: setenv: command not found Then I tried to just run it in the Terminal before calling the script, yet "No command 'setenv' was found". Any idea on what is wrong? Thanks, Lisa On 8 June 2017 at

Re: [Freesurfer] TRACULA -path issue

Hi Anastasia- it is attached- one note is that it is actually a .txt file but i just copied and pasted it into an RTF from our group’s cluster for this purpose. On Jun 7, 2017, at 4:43 PM, Simon, Katrina R mailto:katsi...@sas.upenn.edu>> wrote: Hi Anastasia, when running -prior, I am getting

[Freesurfer] FW: Freeview Application

Just wanted to re-circulate this. Thanks in advance! Panos Panagiotis Fotiadis Research Technologist II J. P. Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA, 02114 T: (617) 643-3869 From: Fotiadis, Panagiot

Re: [Freesurfer] -openmp flag in mri_em_register

Hi Lisa the individual commands don't accept -openmp. Try doing: setenv OMP_NUM_THREADS 2 mri_em_register ... cheers Bruce On Thu, 8 Jun 2017, Lisa Kramarenko wrote: Hello, I am using HCP pipelines and I would like mri_em_register which is being called from a pipeline script to run on 2 c

[Freesurfer] -openmp flag in mri_em_register

Hello, I am using HCP pipelines and I would like mri_em_register which is being called from a pipeline script to run on 2 cores instead on all available ones. I tried to just add an -openmp flag to the command as suggested here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41604.