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

[Paul GRAVEL]

Thanks Vlad,

I didn't get Claude's joke right away (lets just say it was late ;-)!).

Best,

Paul


On Fri, 14 Dec 2012, Vladimir S. FONOV wrote:

> 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
>>>> 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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>>
>
>
>
> -- 
> Best regards,
>
> Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
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