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

[Paul GRAVEL]

Thanks Claude!

Is the new and improved script now part of the minc-toolkit as well?

Best Regards,

Paul


On Wed, 12 Dec 2012, Claude LEPAGE wrote:

> Paul,
>
> I also have a new improved best bestlinreg script. :-) I gave a copy
> of it to Vlad too.
>
> To some, it may sound counter intuitive, but I'm now using -nmi
> (normalized mutual information) for linear registration. It is
> much more robust than xcorr and rather insensitive to variations
> in intensities if N3 is not performed a priori.  A mask is no
> longer necessary for linear registration, although cropping the
> neck usually helps.
>
> Claude
>
>
>>
>> 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
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
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>>
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