[Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1

Hi, If I do: $ freeview -v myfile.nii.gz If I'm pointed at my 6.0.1 freesurfer, this works fine. In 7.2, the freeview window pops up, the loading bar gets to 99%, then then nothing else happens. I'm not sure what to do to debug this further. -- Daniel M. Drucker, Ph.D. Director of IT

Re: [Freesurfer] /usr/pubsw reference in 7.1.1

I should add - the tksurfer call is from within https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLICA . Is there an updated version that doesn’t have this issue? On Jul 15, 2021, at 10:20 AM, Drucker, Daniel mailto:ddruc...@mclean.harvard.edu>> wrote: When running tksurfer in 7.1.1 (from

[Freesurfer] /usr/pubsw reference in 7.1.1

When running tksurfer in 7.1.1 (from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-linux-centos7_x86_64-7.1.1.tar.gz ) , I get: Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This

Re: [Freesurfer] TRACULA trac-all cores/threads

> Hi Daniel - Can you track down which command does this? I suspect that it's > something in the pre- or post-processing, because I haven't added > multi-threading to the main TRACULA executables (yet). trac-all calls trac-preproc calls eddy_openmp Daniel

[Freesurfer] TRACULA trac-all cores/threads

trac-all (TRACULA) seems to use multiple threads/cores. Is there a way to either (a) limit the number, or (b) determine how many it will use, so it can behave appropriately in a cluster? -- Daniel M. Drucker, Ph.D. Director of IT McLean Hospital Imaging Center Harvard Medical School

[Freesurfer] recon-all tries to call mri_relabel_hypointensities -all-info

freesurfer-6.0.1/bin/recon-all line 630 calls: mri_relabel_hypointensities -all-info However, -all-info is not a valid option: $ mri_relabel_hypointensities usage: mri_relabel_hypointensities [options] This program measures a variety of anatomical properties valid options are: -l