[Freesurfer] Not able to install Matlab Runtime (MCR)

2024-07-09 Thread Himanshu Joshi
External Email - Use Caution Dear list, I am trying to install matlab runtime environment (MCR) in $FREESURFER_HOME/freesurfer by using *fs_install_mcr R2019b*. the error is mentioned below: (Jul 09, 2024 12:00:11) The following error was detected while installing *3p/mpich2_glnx

Re: [Freesurfer] Not able to install Matlab Runtime (MCR)

2024-07-09 Thread fsbuild
External Email - Use Caution  It looks like /tmp is running out of space (which can be a separate partition much smaller than the boot partition) to the point where the matlab installer cannot use it.  You can check that with, $ cd /tmp$ df -h . You should be able to delete anyth

Re: [Freesurfer] Not able to install Matlab Runtime (MCR)

2024-07-09 Thread Himanshu Joshi
External Email - Use Caution Dear -R Thankyou for your response. (base) [-- ~]$ cd /tmp (base) [-- tmp]$ df -h . Filesystem Size Used Avail Use% Mounted on */dev/mapper/rhel-root 50G 43G 7.4G 86% /* As per your suggestion we have deleted

Re: [Freesurfer] freeview colormap for volumes

2024-07-09 Thread Wang, Ruopeng
You can create your own color table file and put it in ‘luts’ folder under your FS home directory. There are a few stock color table files in that folder. You can copy and modify one of them to your own. The current color table does not support transparency, though. Ruopeng On Jul 8, 2024, at

[Freesurfer] LME model error: mris_average_surface failed

2024-07-09 Thread Bondi, Daniel
External Email - Use Caution Hello, I am trying to test the LME model created by Bernal using mass-univariate data. Although my entire dataset has about 40 participants with pre- and post-season scans, I am trying to test the pipeline with the data from one subject. On my Mac,

[Freesurfer] Doing math on mgz file

2024-07-09 Thread Aaron Tanenbaum
External Email - Use Caution Is there an equivalent to fslmaths in freesurfer? Thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-ma

Re: [Freesurfer] Doing math on mgz file

2024-07-09 Thread Huang, Yujing
Is this what you are looking for? https://surfer.nmr.mgh.harvard.edu/pub/docs/wiki/mris_calc.help.xml.html From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Aaron Tanenbaum Sent: Tuesday, July 9, 2024 2:07 PM To: Freesurfer Subject: [Freesurfer] Doing math on mgz file Extern

Re: [Freesurfer] Unknown recon-all error - ERROR: reading ../surf/autodet.gw.stats.lh.dat

2024-07-09 Thread Huang, Yujing
Can you send complete recon-all.log? Maybe AutoDetGWStats didn’t run? Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Austin Cooper Sent: Monday, July 8, 2024 11:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unknown recon-all error - ERROR: reading ../surf/au

Re: [Freesurfer] Doing math on mgz file

2024-07-09 Thread Aaron Tanenbaum
External Email - Use Caution Perfect thank you On Tue, Jul 9, 2024 at 1:30 PM Huang, Yujing wrote: > Is this what you are looking for? > > > > https://surfer.nmr.mgh.harvard.edu/pub/docs/wiki/mris_calc.help.xml.html > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >

Re: [Freesurfer] Longitudinal Analysis Error

2024-07-09 Thread Ahmet Kaya
External Email - Use Caution Thank you for your response. I already followed the path in the link provided in your email. All time points are already processed with recon-all. What I could see is the error is regarding that the norm.mgz can not be read, however I can open it with f