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

[Paul GRAVEL]

Many thanks Vladimir!

I will give it a try...

@Simon: I did give bestlinreg_s a try, and it definitely does a better job 
I previously had, i.e. mritotal!

Best Regards,

Paul


On Wed, 12 Dec 2012, Vladimir S. FONOV wrote:

> 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
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>