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

[Vladimir S. FONOV]

Hello,

yes, I included Claude's changes into bestlireg_s , call it with -nmi
option.


On Thu, Dec 13, 2012 at 6:37 PM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>wrote:

> 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 <http://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<http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users>
>>>>
>>>>  ______________________________**_________________
>>> MINC-users at bic.mni.mcgill.ca
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>>>
>>>  ______________________________**_________________
>> MINC-users at bic.mni.mcgill.ca
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>>
>>  ______________________________**_________________
> MINC-users at bic.mni.mcgill.ca
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>



-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com