Re: [Freesurfer] qdec.table.dat error

Check out this article: https://wiki.ubuntu.com/DashAsBinSh /bin/sh is still just a symlink to /bin/bash on Debian. mjp On Oct 8, 2008, at 2:43 PM, Mishkin Derakhshan wrote: Hi Nick, I tried unalias -a and then runnig qdec but it didn't work either. I think the problem is with bash vs. sh

Re: [Freesurfer] tksurfer display problems

Hi all, This is a bug that has baffled me for almost a year now, so today I decided to just attend to it exclusively. I have never understood why, exactly, the anecdotal and illogical fix for the sliver-of-the-brain issue seems to be to install an NVidia graphics card in the afflicted ser

Re: [Freesurfer] tksurfer display problems

hi Sid, This should be done on the server side - where you are processing the data. For example, I have a Dell PowerEdge 1950 that is running 64-bit Debian Gnu/Linux and has Freesurfer/fsfast installed. I log into it from my Mac, which is running os x. So I needed to add those libraries

Re: [Freesurfer] qdec error

It's possible that you are running a Debian-based distro and just don't have libtiff.so.3; but you probably have libtiff.so.4, so you can create a symlink so that libtiff.so.3 points to libtiff.so.4. I have to do this In Debian "etch" and later mjp On Nov 26, 2008, at 4:26 PM, "Siddharth

[Freesurfer] segfault from freeview.bin

Hi all, We are consistently getting segfaults with core dumped from freeview.bin when trying to open MGZ files that are larger than some (undetermined) threshold. We are running the 4.5.0 CentOS 4 x86_64 binary package on Ubuntu 9.04 Workstation. Upon opening freeview and attempting to load on

Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer

Hi Dhruman, I had this problem with a Debian (Etch) system with an ATI card, and the way I got it to work was to install the fglrx driver for the ATI card. I also was missing a bunch of OpenGL stuff, too, but I think the driver was the main issue. I'm unfamiliar with CentOS but these inst

Re: [Freesurfer] libXmu error on cluster

Hi Pedro, What do you see if you run the following command: ldd /usr/lib/libXmu.so.6 Once you fix the problem, if you are running FreeSurfer 4, I *think* you can re-run recon-all with the -make flag and it will just do the processing that got missed. mjp On Mar 22, 2008, at 9:51 PM, Ped

Re: [Freesurfer] error while loading shared libraries:libtiff.so.3

libtiff.so.3 is typically provided by the ia32-libs package in Ubuntu and Debian (and presumably any other Debian-derived distros) So you can install using the following command: sudo aptitude install ia32-libs I'm not sure which binary is doing the complaining, I don't see anything in $FRE

Re: [Freesurfer] tksurfer woes

Hi Matthew, This is the typical symptom of either not having the right OpenGL libraries and/or not having a driver that supports the 3d stuff. That particular chip (ES1000) seems to be an orphan as far as Linux support goes - I haven't found a driver installation package on the ATI/AMD si

[Freesurfer] Segfault in mris_fwhm?

Hi all, I've run into a snag whilst running mris_fwhm: $ mris_fwhm --i /all.nii --s --hemi rh --sum / fwhm.sum rh white Number of vertices 136129 Number of faces272254 Total area 88745.070312 GroupSurface 0 FIX_VERTEX_AREA 1 AvgVtxArea 0.651919 AvgVtxDist 0.883205 Std

Re: [Freesurfer] tksurfer woes

Hi all, FYI, this same problem has been bugging me for several months. Most ATI chipsets have a nice driver installer bundle that, once installed, will let you run tksurfer without a problem. However, this particular chipset, the ES1000, which is the chipset on Dell PowerEdge servers, is

[Freesurfer] Making a surface from the skull?

Hi all, I know this is slightly outside the normal bounds, but I am wondering if there is a way to create a surface from the skull? One of our folks is looking to create some custom-fitted recording chambers for nonhuman primates based on the individual skull. I seem to recall that FS has a way

Re: [Freesurfer] Making a surface from the skull?

inen's MNE website. He uses the watershed code >> to generate boundary models, including skull. Or just try out mri_watershed >> with -surf I think (it's covered in the help, at least a bit) >> >> cheers >> Bruce >> >> >> On Fri, 1 Oct 20