Re: [Freesurfer] Pial Edit on Atrophied Brain

2010-10-05 Thread Soon Hock Wei
mris_make_surfaces command) that I can adjust to allow for more expansion? Meaning the pial boundary will be "pushed" further from WM surface? I know the end-result maybe be worse but just for the sake of curiosity. Thanks! Regards, Hock Wei SOON -Original Message----- From: Soo

[Freesurfer] Pial Edit on Atrophied Brain

2010-09-27 Thread Soon Hock Wei
Dear All:   I am working on MRI images of subjects suffered from dementia. In severe cases, atrophy is observed where the white matter loss causes reduced white/gray differentiation. Hence, the pial surface generated from the autorecon2 does not include what is clearly atrophied cortical tiss

[Freesurfer] mri_convert multiple sequences

2010-08-25 Thread Soon Hock Wei
Dear All:   I have the Siemens dicom files (for multiple sequences, both structural and functional, e.g. MPRAGE, T2, BOLD etc) in a CD, and I would like to convert them into analyze format using mri_convert.   Please kindly correct me if I am wrong: Am I right to say that I need to call:   mri_c

[Freesurfer] From mgz to m3z

2010-08-24 Thread Soon Hock Wei
Dear All:   Can any kind soul please enlighten me on this: If let's say I am given these mgz files:   transforms/talairach.m3z.inv.x.mgz transforms/talairach.m3z.inv.y.mgz transforms/talairach.m3z.inv.z.mgz (the output from -careginv)   Is it possible for me to recover the

[Freesurfer] File Format for talairach.m3z

2010-08-10 Thread Soon Hock Wei
Dear All: I am a new user of FreeSurfer and I am wondering what is the file format for talairach.m3z (i.e. the output of mri_ca_register)? I couldn't find this information in FreeSurfer Wiki. In addition, I would like to know how can I use this talairach.m3z to check the accuracy of non-linear