Re: [Freesurfer] freeview command for displaying selected labels

2020-06-02 Thread Schranzer René
External Email - Use Caution Hi Ruopeng, ok, thanks. Best, René Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Ruopeng Wang Gesendet: Freitag, 29. Mai 2020 16:24 An: Freesurfer support list Betreff: Re: [Freesurfer] freeview command for displaying selected labels

[Freesurfer] New option to run (Freeview) under Windows 10

2020-06-02 Thread fsbuild
External Email - Use Caution Hello Freesurfer List Subscribers, Please be aware we have added another option to enable Freeview to run under Windows 10. In addition to the VirtualBox Ubuntu disk image you can download, there is now documentation about how to run Freeview in a Li

Re: [Freesurfer] Bbregister misalignment {Disarmed}

2020-06-02 Thread Douglas N. Greve
If you upload the data, I'll take a look. Upload both the structural and the fMRI. See instructions below From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log  into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu I

[Freesurfer] job add MR-Physicist/Engineer

2020-06-02 Thread Michael Marxen
External Email - Use Caution Dear colleagues, we are currently looking for an MR-Physicist/Engineer at the post-doctoral level at the TU Dresden. Details can be found here: https://www.verw.tu-dresden.de/StellAus/download.asp?file=06-2020\Krug_WIMI_eng_210220_160.pdf Please,

Re: [Freesurfer] Bbregister misalignment {Disarmed}

2020-06-02 Thread Mason Wells
External Email - Use Caution Just a follow up here. I tried the command below on a machine with v.6, and the flag was recognised, but the registration was still off. No change to the output with the flag included. Mason T Wells, MSc PhD student School of Optometry and Vision Sci

Re: [Freesurfer] Bbregister misalignment {Disarmed}

2020-06-02 Thread Mason Wells
External Email - Use Caution Hi Doug, I have FS v6.0 and tried the following command: ERROR: Flag --init-coreg unrecognized. --s PPT_001 --feat /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/ --int /cubric/data/c1749990/PhD/Data/PMA_re

Re: [Freesurfer] using freesurfer, Is it ok to compare cortical thickness for group-1 people from one scanner, while control group from another acanner

2020-06-02 Thread Douglas N. Greve
Generally, this is a bad idea as it will be impossible to tell scanner-induced diffs from group-induced diffs On 6/1/2020 11:36 PM, John wrote: External Email - Use Caution Hi friends, Using freesurfer, Is it ok to compare cortical thickness for group-1 people from one scanner, while

Re: [Freesurfer] Bbregister misalignment {Disarmed}

2020-06-02 Thread Douglas N. Greve
Right now, I'm just guessing what the problem is (I'm speculating that it is FSL FLIRT). You could download just the new bbregister and mri_coreg to your VM and see if it works. On 6/2/2020 6:40 AM, Mason Wells wrote: External Email - Use Caution I am using version 5.3, this is the

Re: [Freesurfer] Bbregister misalignment {Disarmed}

2020-06-02 Thread Mason Wells
External Email - Use Caution I am using version 5.3, this is the version on the virtual machine I am working from. I can ask about an updated version, but is there a way to fix this on v5.3 in the meantime? Mason T Wells, MSc PhD student School of Optometry and Vision Sciences &

Re: [Freesurfer] Problems with freesurfer 7.1.0 and MacOS

2020-06-02 Thread Angela Favaro
External Email - Use Caution Dear freesurfer experts, I found the same problems with recon-all (segmentation failure) using a Mac OS Sierra (10.12) and the same failures (more than 10% of cases) with the command: recon-all -base template -tp subj001 -tp subj002 -all Hope it is