Re: [Freesurfer] mri_mask problem

2011-03-17 Thread Gabriel Go.Es.
That works!!! Thank you, Gabriel > Date: Tue, 15 Mar 2011 14:34:00 -0400 > From: gr...@nmr.mgh.harvard.edu > To: gabriel...@hotmail.com > CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; > ni...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_mask problem > > For mri_

[Freesurfer] scatterplot saving problem with qdec 1.4

2011-03-17 Thread johanna feiler
Dear FreeSurfer experts, I'm using qdec 1.4 and I want to save the scatterplot with the "save GDF plot as postscript" button. It pretends saving a file but in fact it doesn't. Instead, in the terminal window following error message appears: wrong # args: should be "FsgdfPlot_SaveToPostscri

[Freesurfer] mri_normalize

2011-03-17 Thread Juranek, Jenifer
I'm running a normal brain through FSv5.0.0 using the -cw256 flag and encounter a problem at the mri_normalize stage. The nu.mgz file looks fine...WM regions have intensity values >110; cortical GM regions have intensity values 70-106; csf intensity values are around 60. The output file (T1.mgz)

Re: [Freesurfer] mri_normalize

2011-03-17 Thread Bruce Fischl
Hi Jenifer, I just fixed this bug in 5.1. Does this subject have a lot of damaged white matter? You can download a dev version of mri_normalize or wait for 5.1 cheers Bruce On Thu, 17 Mar 2011, Juranek, Jenifer wrote: > I'm running a normal brain through FSv5.0.0 using the -cw256 flag and >

[Freesurfer] recon-all

2011-03-17 Thread leonardo kay
Hi I have been trying to import my data and create a subject directory using the following command: recon-all -i -s replacing with the path where my T1 structural nifti is allocated, and -s with the name of the subject (susu), which is supposed to be the name of the directory too. But a

Re: [Freesurfer] recon-all

2011-03-17 Thread Bruce Fischl
Hi Leonardo, can you send the actual command? You should only replace the <> part, not the -i in the cmdline (same for the -s). Bruce On Thu, 17 Mar 2011, leonardo kay wrote: > Hi > > I have been trying to import my data and create a subject directory using > the following command: > > recon-a

Re: [Freesurfer] hippocampal subfields

2011-03-17 Thread Thomas Wolbers
Sorry to repost this question, but it would be great to know if there is a chance the automated segmentation of hippocampal subfields might be incorporated in Freesurfer any time soon. Cheers, Thomas -- - Dr. rer. nat. Thomas Wolbers Seni

[Freesurfer] [New release] - iSurf Brainview 2.1.0

2011-03-17 Thread Pedro Paulo de Magalhães Oliveira Junior
Today it was released a new major upgrade of iSurf Brainview. (2.1.0) New features: - New Atlas: Chistophe Destrieux 2009 Atlas - Improved Interface - Retina Display - iOS 4.3 As usual suggestions are welcome. Upcoming features will include 3D visualization. The link for download is: http://it

[Freesurfer] using multiple processors with freesurfer?

2011-03-17 Thread jim kroger
Hello, I just downloaded freesurfer and am processing some of my data. I am using an 8 core machine, but I'm guessing freesurfer is using only one processor. Can you point me to information about taking advantage of multi cores when using freesurfer, if that is possible? Many thanks, Jim Kroger NMS

Re: [Freesurfer] CUDA installation

2011-03-17 Thread Knut J Bjuland
Hi You will have to use either deb package or the cuda installer from nvidia. since I have only used the package from nvidia. You should installed using sudo. I did the follwoing protocoll to install cuda. Chmod +x Cuda, the sudo ./cuda. The you will have to add the path to your libarypath.

Re: [Freesurfer] [New release] - iSurf Brainview 2.1.0

2011-03-17 Thread Rudolph Pienaar
If I had an iOS device, this sounds like a wonderful app, Pedro... Any chance of an Android version?? :-P -=R On 3/17/11 16:42 , Pedro Paulo de Magalhães Oliveira Junior wrote: > Today it was released a new major upgrade of iSurf Brainview. (2.1.0) > > New features: > - New Atlas: Chistophe Dest