Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

mri_convert questions?
by Brain Apprentice 14 Jan '10

14 Jan '10

Hello, I was just wondering if there was a way in mri_convert to conform a MRI scan so that the output file is 16-bit? The reason I ask is that I am trying to create dual pipelines. One pipe for Freesurfer and the other pipe for SPM and it would be nice to use mri_convert to generate the data for both from DICOM files. Thanks, BA

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Keyboard problem in FreeSurfer
by XJ Kang 14 Jan '10

14 Jan '10

Hi, I am using FreeSurfer 4.5, on a 64-bit Dell Precision workstation. The OS is Centos 5.4. I cannot input anything in tkmedit using my keyboard. I can only input curvature file names in tksurfer, but not overlay file names and threshold values. I searched the mailing archives, same thing happened to Hiroyuki (See below). I am wondering if this is a problem for 64-bit machine. Any suggestions? Thank you. XJ Kang >Dear all, > >I am running freesurfer 4.5 on Ubuntu9.10(64bit). >Is anybody experiencing " lost keyboard " problem? >I cannot put any number in tkmedit and tksurfer using keyboard. > >Thank you. > >Hiroyuki

4 3

Re: [Freesurfer] poll question: Mac OS Tiger users
by Ed Gronenschild 14 Jan '10

14 Jan '10

Hi Nick, I'm using Freesurfer on different Macs, of which one with Tiger OS and ppc. So, I kindly ask you to continue support for Tiger OS and ppc for at least this year. Ed On 13 Jan 2010, at 23:14, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > for the Mac OS users out there: > > who still needs a Tiger OS build of freesurfer? and on what processor > (intel or ppc)? > > i'd like to discontinue support for Tiger (and redirect efforts toward > working with Snow Leopard), but if enough people still need the Tiger > build then we can keep our creaky-old machine around to do this. > > Nick

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design is ill-conditioned
by Maximilien Chaumon 13 Jan '10

13 Jan '10

Hi freesurfers, I'm trying to run an estimation with my last subject and get stuck with a ERROR: design is ill-conditioned I can imagine this means that my design misses something bu I can't find what. Conditions all have events in all runs, time points are equally spaced. Here's the log of the session /autofs/space/bomba_016/users/chaumon/log/selxavg3-sess-bold-Analyse_Simple_Confidence-091215135329.log Thanks for any help, Max

2 1

poll question: Mac OS Tiger users
by Nick Schmansky 13 Jan '10

13 Jan '10

for the Mac OS users out there: who still needs a Tiger OS build of freesurfer? and on what processor (intel or ppc)? i'd like to discontinue support for Tiger (and redirect efforts toward working with Snow Leopard), but if enough people still need the Tiger build then we can keep our creaky-old machine around to do this. Nick

1 1

a freeview bug ?...
by Gonzalo Rojas 13 Jan '10

13 Jan '10

Hi: I load orig.mgz using freeview application, but when I try to load lh.thickness or rh.thickness file, freeview quits unexpectedly... it is a freeview bug ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

2 3

a freeview bug ?...
by Gonzalo Rojas 13 Jan '10

13 Jan '10

Hi: I have freesurfer 4.4.0... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

1 0

modification of tksurfer and tkmedit palettes
by Gonzalo Rojas Costa 13 Jan '10

13 Jan '10

Hi: I will write my question in another way: in which file could I find the palette that tksurfer and tkmedit uses to display overlay data ?... because I want to create other palettes... Sincerely, Gonzalo Rojas Costa

4 4

tkmedit and tksurfer volume display problem in Ubuntu 9.04
by Miguel Burgaleta 13 Jan '10

13 Jan '10

Hi again, I am experiencing some problems when testing my freesurfer installation in Ubuntu 9.04. When I run tkmedit and tkmsurfer the interface opens OK, but the volume display window behave in a weird manner in both cases: it appears but quickly disappears. In tkmedit, if I click on some of the buttons to choose a view (for instance, axial), the volume window appears but it disappears if I move the cursor out of the selected button. Is this problem familiar to anyone? Thanks in advance for any help! Miguel

3 3

Freesurfer Ubuntu 9.04 installation
by Miguel Burgaleta 13 Jan '10

13 Jan '10

Dear all, This is a technical, linux-related question: I have just installed Freesurfer in a computer running Ubuntu 9.04. When testing the installation, I get an error message right in the first step. I try to do: tkmedit bert orig.mgz And the message I get is: tkmedit.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory I was wondering if some of you experts can say how to solve this? Thanks a lot in advance, Miguel

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