[Freesurfer] Freesurfer compatibility Fedora 12?

Hi FreeSurfer Experts, I am working on a cluster which ran until recently on the Linux OS Fedora 4. Since the upgrade to Fedora12 I can no longer launch tkmedit whereas it worked fine on the previous OS(fedora4). The following error appears: GLUT: Fatal Error in tkmedit.bin: visual with ne

Re: [Freesurfer] Freesurfer compatibility Fedora 12?

Check: 1) The resolution of monitor in Fedora FC12 and color depth 2) The drivers for your video board (ATI/NVidia) -- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- For mobile: http://www.netfilter.c

[Freesurfer] Number of time points

Hi, > > I was trying out a code to generate optimal sequences using optseq2. The code > is as follows: > > > optseq2 --ntp 300 --tr 2 \ > --psdwin 0 12 1 \ > --ev one 1 20 \ > --ev two 1 15 \ > --ev three 1 15 \ > --ev four 1 50 \ > --ev five 1 50 \

Re: [Freesurfer] Number of time points

you should not interpret each line as a time point. Each line is a stimulus presentation. You have specified that the presentations are 1 sec long and can occur at an time divisible by 1 sec (--psdwin 0 12 1), so you could have as many as 600 lines. BTW, I would probably go longer than 12 sec f

Re: [Freesurfer] Number of time pointsTuesday, May 18, 2010 12:17 PM

Hi Doug, Thank you very much for the reply. The question that I have now is, how do I distribute my time points between the events and also specify a fixed number of time points for the "NULL" cases? Thanks and Regards, Usha you should not interpret each line as a time point. Each line is a s

Re: [Freesurfer] mri_aparc2aseg on a custom annotation

Hi Dough, On Monday 17 May 2010 22:29:28 Douglas N Greve wrote: > So is the problem that cortex is 2000 every where including your label Yes this is the case, but I have already found a way around to get to where I wanted. mri_label2voi --help has the example which helped me. Thanks anyway, Ma

[Freesurfer] How to get deformation maps in surface-based registrations

Hi, all, I have a question regarding how to get the deformation map in surface-based registration. I am wanting to use mris_register to align two surfaces. Can I get the deformation maps describing the vertex-to-vertex correspondence? How can I get it? Thanks a lot. Best, Xiaojing _

Re: [Freesurfer] How to get deformation maps in surface-based registrations

Hi Xiaojing, the deformation map is the difference between the ?h.sphere.reg and the ?h.sphere. I guess you would want to represent them as arcs of great circles. cheers, Bruce On Tue, 18 May 2010, Xiaojing Long wrote: > Hi, all, > > I have a question regarding how to get the deformation map i

Re: [Freesurfer] How to get deformation maps in surface-based registrations

Hi, Bruce, Thanks a lot for replying me. Do I have to create the deformation file by myself? Or can it be generated from some option set in mris_register? Thanks again. Best, Xiaojing 2010/5/18 Bruce Fischl > Hi Xiaojing, > > the deformation map is the difference between the ?h.sphere.re

Re: [Freesurfer] Number of time pointsTuesday, May 18, 2010 12:17 PM

I don't understand your question. Can you elaborate? Tadimeti, Usha wrote: > Hi Doug, > > Thank you very much for the reply. The question that I have now is, how do I > distribute my time points between the events and also specify a fixed number > of time points for the "NULL" cases? > > Thanks

Re: [Freesurfer] How to get deformation maps in surface-based registrations

I don't think we have anything to create the deformation field explicitly, unless Thomas Yeo (ccd) does. cheers Bruce On Tue, 18 May 2010, Xiaojing Long wrote: > Hi, Bruce, > > Thanks a lot for replying me. > > Do I have to create the deformation file by myself? Or can it be generated > from >

Re: [Freesurfer] How to get deformation maps in surface-based registrations

I don't have it either. Regards, Thomas On May 18, 2010, at 4:51 PM, Bruce Fischl wrote: > I don't think we have anything to create the deformation field > explicitly, unless Thomas Yeo (ccd) does. > > cheers > Bruce > > On Tue, 18 May 2010, Xiaojing Long wrote: > >> Hi, Bruce, >> >> Thanks a

[Freesurfer] OASIS database difference aseg volumetry...

Hi: I downloaded a dataset image from OASIS (OAS1_0068_MR1)... I reprocessed with Freesurfer v4.5.0 (recon-all -legacy command) But, there are differences between the old and new aseg.stats file... for example, the ICV: 1433107.255467 (old), 1328556.632821 (new)... left Hippocampus: 4130.0 (

Re: [Freesurfer] How to get deformation maps in surface-basedregistrations

It is possible to do this sort of thing in Caret (using the FreeSurfer registration); one can create a deformation map between sphere and sphere.reg. What do you need the deformation map for? Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-

[Freesurfer] Freesurfer for stroke subjects?

Hello Freesurfers We are going to handle some subjects with stroke or subjects who receives a surgery to remove brain tumors. I just wonder whether it is possible to use freesurfer for those subjects and how the surface registration is affected. Best, Han _