[Freesurfer] questions

Hello All, I have 2 questions I hope someone can help me with. 1) Is it possible to plot on a surface a set of arbitrary points in the coordinate frame of an anatomical volume? In other words if I have a set of x,y, and z points (not voxel indices: e.g. sub-voxel coordinates) can I plot the

[Freesurfer] white matter surface leakage

Dear List, I am having a problem with mri_normalize. The problem is that after normalization the white matter areas in my volume have expanded and leaked into area that should be grey matter, is there a way to place control points for grey matter? Thanks paul ___

[Freesurfer] skull strip for monkeys

Hello All, I am having a very difficult time getting skullstrip to work on my monkey anatomical data set. Are there any suggestions on how to get it to work properly? Thanks in advance Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.e

[Freesurfer] Re: Freesurfer Digest, Vol 37, Issue 16

Hi Bruce, regarding the high res recon, you mention that you can change the info w/o changing the data using mri_convert, and this should keep mri_normalize from conforming the data to 1mm voxels? Do you know the commands that accomplish this? I have tried changing the file to COR format and

[Freesurfer] recon-all problem

Hello all, I run recon-all and get this problem: - Nu Intensity Correction Tue Sep 6 13:04:59 EDT 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 i_ras = (-1, -0, 0) j_ras =

[Freesurfer] question

Hello list, I had a question about unpacksdcmdir. I am trying to get freesurfer/fs-fast up and running on my off-site linux box. It goes through the motions until I try to unpack my raw allegra data, then it stops on me and gives the following error: error: reading ../...path to raw data.../1