[MINC-users] Registering 3T MRI to stereotaxic space

[Vladimir S. FONOV]

Hello Paul,

you can try running "standard pipeline" - also distributed with 
minc-toolkit :

1. source the environment

source /ipl/quarantine/experimental/2012-09-18/init.sh for bash
or
source /ipl/quarantine/experimental/2012-09-18/init.csh

2. run the pipeline:


/ipl/quarantine/experimental/2012-09-18/pipeline/standard_pipeline.pl 
<subject> <visit> <t1w.mnc> --prefix <out> --disable_nonlinear 
--model_dir /ipl/quarantine/models/icbm152_model_09c --model 
mni_icbm152_t1_tal_nlin_sym_09c

it will perfom linear registration and brain extraction using BEaST, the 
output files  will following:

<out>/<subject>/<visit>/tal/tal_xfm_<subject>_<visit>_t1w.xfm - linear 
transformation from native space to standard space


<out>/<subject>/<visit>/tal/tal_<subject>_<visit>_t1w.mnc - normalized 
t1w scan in standard space space

<out>/<subject>/<visit>/tal/tal_comp_msk_<subject>_<visit>.mnc - brain mask.

On 12-12-11 06:59 PM, Paul GRAVEL wrote:
> Dear All,
>
> I am trying to estimate the transformation parameters to co-register an
> MRI acquired on the 3T MR machine here at the MNI, and it seems that
> mritotal doesn't do such a good job (I used it before for scans acquired
> on the 1.5T machine without any problems). Therefore, I was wondering if
> anyone would have the latest procedure (and is willing to share ;-)! )
> to coregister an MRI from the 3T to stereotaxic space.


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com