[MINC-development] nonlinear .xfm for t1 (Kristi Drudik)

[Kristi Drudik]

Hi Claude,
Thank you very much for your reply. Will play around with CIVET now.
Best,
Kristi

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Today's Topics:

   1. nonlinear .xfm for t1 (Kristi Drudik)
   2. Re: nonlinear .xfm for t1 (Claude LEPAGE)


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Message: 1
Date: Mon, 28 Aug 2023 17:20:19 +0000
From: Kristi Drudik <kristina.drudik at mail.mcgill.ca>
To: "minc-development at bic.mni.mcgill.ca"
        <minc-development at bic.mni.mcgill.ca>
Subject: [MINC-development] nonlinear .xfm for t1
Message-ID:
        <YT2PR01MB8200BB97494B3746F0D6FFCBCBE0A at YT2PR01MB8200.CANPRD01.PROD.OUTLOOK.COM>

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Hello!

Please excuse my ignorance. I would like to generate a non-linear .xfm file for my subjects' native T1 using the icbm152_nlin_asym_09c. Would the following command suffice or am I missing options? Not sure what values I'd need to put for options like:
-weight
-stiffness
-similarity
-sub_lattice....etc...

minctracc ${subjDir}/T1.mnc ${mni_template} ${subjDir}/nonlin.xfm -nonlinear -est_translation -est_center -clobber

Thank you very much for clarifying.

Best,
Kristi
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Message: 2
Date: Mon, 28 Aug 2023 13:29:08 -0400
From: Claude LEPAGE <claude at bic.mni.mcgill.ca>
To: minc-development at bic.mni.mcgill.ca
Subject: Re: [MINC-development] nonlinear .xfm for t1
Message-ID: <202308281729.37SHT8No018398 at login1.bic.mni.mcgill.ca>
Content-Type: text/plain; charset="UTF-8"

Hi Kristi,

You can start by looking at the non-linear registration in the CIVET pipeline.

https://github.com/aces/CIVET/tree/master/progs

linear registration: bestlinreg.pl
non-linear registration: best1stepnlreg.pl

You have to start with linear registration, then proceed with non-linear.
Non-linear will work well if you are close to the target.

These scripts outline registration recipes with prescribed weight, stiffness, similarity, sub-lattice, etc. It's a good starting point.

NOTE: You can also use ANTs in the minc-toolkit as an alternative approach.

Claude

>
> Hello!
>
> Please excuse my ignorance. I would like to generate a non-linear .xfm
> file=  for my subjects' native T1 using the icbm152_nlin_asym_09c.
> Would the foll= owing command suffice or am I missing options? Not
> sure what values I'd nee= d to put for options like:
> -weight
> -stiffness
> -similarity
> -sub_lattice....etc...
>
> minctracc ${subjDir}/T1.mnc ${mni_template} ${subjDir}/nonlin.xfm
> -nonlinea= r -est_translation -est_center -clobber
>
> Thank you very much for clarifying.
>
> Best,
> Kristi


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