Re: [Freesurfer] talairach.xfm p=0.0000 error, brainmask.mgz not created

Hi Prantik, do you process the data directly from dicoms? If you bring up the orig.mgz in tkmedit does it orient properly? cheers Bruce On Tue, 11 Aug 2009, Prantik Kundu wrote: > Hello > > In default FS usage, all of the MPRAGE's from this particular study > that I'm analyzing are dying with

Re: [Freesurfer] MS lesions

Hi Miguel, I think Koen Van Leemput (ccd) has some tools for this, but in general we don't characterize MS lesions much, although we do generically label damaged white matter. cheers, Bruce On Tue, 11 Aug 2009, Jose Soares wrote: Hi, what kind of information can I get with FreeSUrfer abou

Re: [Freesurfer] Clusterwise correction

1) The smoother the data, the more likely a cluster will be found by chance. When the data are created, they start with some smoothness level. When you smooth them you add more. So you need to match the total level of smoothing when you do the simulations, otherwise your clusters will be way to

[Freesurfer] talairach.xfm p=0.0000 error, brainmask.mgz not created

Hello In default FS usage, all of the MPRAGE's from this particular study that I'm analyzing are dying with the error shown below. MPRAGE's from other studies appear to be processed just fine. The MPRAGEs from the experiment that FS is failing on are generally of higher quality than those

Re: [Freesurfer] MS lesions

I don't think FreeSurfer will give any direct measure of MS. In the wiki page of FreeSurfer there's a paper about MS: http://www.nmr.mgh.harvard.edu/~fischl/reprints/Brain2003v126p1734Sailercorticalthickness.pdf --- Pedro Paulo de M. Oliveira

[Freesurfer] Clusterwise correction

Hello all, I have a couple of questions regarding the way the cluster correction simulation in freesurfer works. I've read the wiki pages on the subject, but if I've missed something and any of this is answered elsewhere please let me know. My technical knowledge of these things is not great

[Freesurfer] MS lesions

Hi, what kind of information can I get with FreeSUrfer about MS lesions? Number of lesions? Lesion volume? Thanks, Miguel. Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbusca

Re: [Freesurfer] mri_surf2surf --cortex

Your 2nd description is correct. Note that the value of vertices outside of the mask are NOT changed (ie, they are not set to 0). doug DRC SPM wrote: > Dear FreeSurfers, > > Please can you explain how mri_surf2surf's --cortex option for > smoothing is implemented? > > I assumed it would be along

Re: [Freesurfer] Less smoothing in version 4.1 than 4.0?

Yes, this is a result of our confusion as to how to handle the changes in area in the average subject. You can actually specify the number of iterations directly in mri_surf2surf with the --nsmooth-in command. doug DRC SPM wrote: > Dear FreeSurfers, > > My apologies if this is mentioned in the

[Freesurfer] mri_surf2surf --cortex

Dear FreeSurfers, Please can you explain how mri_surf2surf's --cortex option for smoothing is implemented? I assumed it would be along the following lines: - mask the data to zero-out the medial wall - smooth this masked data - smooth the mask itself - divide the smoothed data by the smoothed

[Freesurfer] Less smoothing in version 4.1 than 4.0?

Dear FreeSurfers, My apologies if this is mentioned in the release notes, but I couldn't find it with a quick search. I'm using the following command to smooth some data: mri_surf2surf --hemi rh --s average --sval in.mgh --fwhm 20 --tval out.mgh Under FreeSurfer version 4.0.3, part of the outpu

Re: [Freesurfer] converting .img to .nii

It might not be oriented correctly. You can discern for yourself whether A/P and S/I are right, but you might not be able to tell L/R. doug Ritobrato Datta wrote: > Hello All, > > I am trying to convert > > [...@home] /jet/subjects/002/Anatomy> mri_convert nAnatomical_fsl_FLOAT.img > nAnatomi

Re: [Freesurfer] ROI reliability

Hi Bruce, Just chiming in here given that I've worked on a similar project for brad (hi res hippocampus segmentation). essentially we want to use the hires volumetric data to make a refined segmentation of the amygdala. such a segmentation is not really possible to do given the visual inte

[Freesurfer] converting .img to .nii

Hello All, I am trying to convert [...@home] /jet/subjects/002/Anatomy> mri_convert nAnatomical_fsl_FLOAT.img nAnatomical_fsl_FLOAT.nii mri_convert nAnatomical_fsl_FLOAT.img nAnatomical_fsl_FLOAT.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from nAnatomical_fsl_F

Re: [Freesurfer] question about talairach transform used in skullstrip

Guang, brainmask.auto.mgz (and all the volume files produced in the recon-all stream) remain in native space. you can add -nowsatlas after -skullstrip to recon-all to see the results without the atlas (results differ depending on the input). the tal transforms are used only to align the atlas, a

Re: [Freesurfer] tksurfer display

Corinna, run this to ensure the driver is up-to-date: sudo /sbin/init 3 to get login prompt login sudo /usr/bin/nvidia-installer update Nick On Tue, 2009-08-11 at 10:01 -0400, corinna bauer wrote: > The graphics card is: nVidia Corporation NV34 [GeForce FX 5200] (rev > a1). As far as I kno

[Freesurfer] question about talairach transform used in skullstrip

Hi, there, In the skullstrip step, mri_em_register command is called and a talairach_with_skull.lta file is produced. This lta file will be used in the following mri_watershed command. My questions are: (1) Once we got the brainmask.auto.mgz, which command we can use to inverse the

Re: [Freesurfer] reinstalling freesurfer

You can simply execute: rm -rf /usr/local/freesurfer If your freesurfer installation is in another directory, change the command above accordingly --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- No

[Freesurfer] reinstalling freesurfer

Hello Experts, I apologise for the stupidity of this question, but I am not used to using Linux at all, but I need to uninstall my Freesurfer and then reinstall it, however, I have no idea how to uninstall in Linux. Can someone possibly assist me in this problem? I'd be extremely grateful. Tha