[Freesurfer] Talairach QA check failed

Dear FS experts I tried to preprocess two T1-w. scans from a 7T scanner (dimensions 448x448x180; resolution 0.5x0.5x0.8mm) but the Talairch quality check failed. Fri Jan 25 08:47:06 CET 2008 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #--

Re: [Freesurfer] which image is the best

Hi: Your description of the problem looks to me like there's some trouble with the interpretation of the 1404 mm dimension. It seems very unlikely that you have a scan that actually covers 1404 mm, so there must be a problem here. I would advise reading the header of the scan, which might requi

Re: [Freesurfer] which image is the best

If you can setup your scanner, these parameters are optimal: http://www.nmr.mgh.harvard.edu/~andre/Sequences/SagMPR8Min.html On Fri, 2008-01-25 at 11:32 +0800, Feng-Xian Yan wrote: > Hi, >I have a problem about which image is the best to run. I had ran > the 1.5T data in freesurfer. Because

[Freesurfer] which image is the best

Hi, I have a problem about which image is the best to run. I had ran the 1.5T data in freesurfer. Because the contrast of the 1.5T data was too bad, I use the 3T data and rerun again. When I run, it says the warning, WARNING The phys

Re: [Freesurfer] vertex neighbourhood

If you want to write your own program to do this, you can use the ANN lib at http://www.cs.umd.edu/~mount/ANN/ - Original Message - From: <[EMAIL PROTECTED]> To: Sent: Friday, January 25, 2008 5:02 AM Subject: [Freesurfer] vertex neighbourhood > hi surfers, > Imagine that I need to k

Re: [Freesurfer] vertex neighbourhood

Well said. You can generate a surface data file with all 0s except your target vertex with mri_volsynth, something like: mri_volsynth --vol yourfile.mgh --temp $SUBJECTS_DIR/yoursubject/surf/lh.curv --pdf delta --delta-crsf vertexno 0 0 0 you can smooth it with mri_surf2surf. You can get the

RE: [Freesurfer] vertex neighbourhood

It is easier to find the neighborhood for a given number of steps away from the vertex of interest. One easy way is to set the value of a single vertex, smooth for a particular number of iterations, and then select the non-zero vertices. If you smooth 5 times, you will get 5 steps away. The

[Freesurfer] vertex neighbourhood

hi surfers, Imagine that I need to know what are the closest N vertices (let's say n=100) to a given vertex (i mean two dimentionsal neighourhood on surfaces) . Any idea how to do that? anybody has a written code for this? cheers nima ___ Freesurfer maili