Re: [Freesurfer] using -nuintensitycor-3T flag with v-5.0.0

2010-08-18 Thread Nick Schmansky
1. correct, or more easily, you can just run: recon-all -s -all -nuintensitycor-3T 2. correct, there are no parameters with that flag. that flag itself adjusts the parameters to nucorrect (which will match those described in the paper linked in the release notes). let us know if it improves yo

[Freesurfer] [freesurfer] installation

2010-08-18 Thread Ignacio Letelier
Hi all I'm a new freesurfer user and I have some troubles installing the program. after moving to cd /usr/local I typed *freesurfer-virtual:~>* tar xzvf freesurfer-Linux---full.tar.gz replacing - with freesurfer-Linux-centos4-stable-pub-v4.3.1 I get the following error message Cannot >>

Re: [Freesurfer] [freesurfer] installation

2010-08-18 Thread Douglas N Greve
Is that file in that directory? What size is it? Do you have write permissions to that folder? doug Ignacio Letelier wrote: > Hi all > > I'm a new freesurfer user and I have some troubles installing the > program. > > after moving to > cd /usr/local > > I typed *freesurfer-virtual:~>* tar xzvf

[Freesurfer] installation of v5.0.0 without erasing v.4.5.0

2010-08-18 Thread Gonzalo Rojas Costa
Hi: Can I install freesurfer v5.0.0 without erasing v.4.5.0 ?... Because I want to test some new features but I need to continue using v.4.5.0... I installed v.4.5.0 in /usr/local/freesurfer... Sincerely, Gonzalo Rojas Costa ___ Freesurfer maili

Re: [Freesurfer] installation of v5.0.0 without erasing v.4.5.0

2010-08-18 Thread Nick Schmansky
yes, you can untar the .tar.gz file in any directory. its only the FREESURFER_HOME setting that matters. you set that, then call $FREESURFER_HOME/SetUpFreeSurfer.csh. n. On Wed, 2010-08-18 at 12:29 -0400, Gonzalo Rojas Costa wrote: > Hi: > > Can I install freesurfer v5.0.0 without erasing

[Freesurfer] Fwd: [freesurfer] installation

2010-08-18 Thread Ignacio Letelier
Sorry Doug I forgot to send the entire email thread. Now, could you please help me with the installation. Best regards. Forwarded conversation Subject: [freesurfer] installation From: *Ignacio Letelier* Date: 2010/8/18 To: freesurfer@nmr.mgh.harvard.edu Hi all I'm

[Freesurfer] User-defined colormaps

2010-08-18 Thread Hansen, Kathleen (NIH/NIMH) [F]
Hello, If we are visualizing fmri surface data with tksurfer, how can we load our own user-defined colormaps? If this is not possible in tksurfer, is it possible using some other Freesurfer function? Thank you, Kathleen ___ Freesurfer mailing list Fre

Re: [Freesurfer] User-defined colormaps

2010-08-18 Thread Douglas N Greve
sorry, not possible in tksurfer. Hansen, Kathleen (NIH/NIMH) [F] wrote: > Hello, > > If we are visualizing fmri surface data with tksurfer, how can we load our > own user-defined colormaps? If this is not possible in tksurfer, is it > possible using some other Freesurfer function? > > Thank you, >

Re: [Freesurfer] Fwd: [freesurfer] installation

2010-08-18 Thread Douglas N Greve
Hi Ignacio, Is that file, ie, freesurfer-Linux-centos4-stable-pub-v4.3.1.tar.gz, in that directory? What is the size of freesurfer-Linux-centos4-stable-pub-v4.3.1.tar.gz? Do you have write permissions to that folder? doug Ignacio Letelier wrote: > Sorry Doug I forgot to send the entire email

[Freesurfer] question about the -zgez flag with mri_convert

2010-08-18 Thread Mehul Sampat
Hi Folks I use mri_convert to create nifti files from the dicom images from a 3T GE scanner. One of the option for mri_convert is "-zgez" with the following description from the mri_convert help: " -zgez, --zero_ge_z_offset set c_s=0 (appropriate for dicom files from GE machines with isocenter s