From kristina.drudik at mail.mcgill.ca Mon Aug 28 13:20:19 2023 From: kristina.drudik at mail.mcgill.ca (Kristi Drudik) Date: Mon, 28 Aug 2023 17:20:19 +0000 Subject: [MINC-development] nonlinear .xfm for t1 Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From claude at bic.mni.mcgill.ca Mon Aug 28 13:29:08 2023 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Mon, 28 Aug 2023 13:29:08 -0400 Subject: [MINC-development] nonlinear .xfm for t1 In-Reply-To: Message-ID: <202308281729.37SHT8No018398@login1.bic.mni.mcgill.ca> 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 From kristina.drudik at mail.mcgill.ca Wed Aug 30 11:05:07 2023 From: kristina.drudik at mail.mcgill.ca (Kristi Drudik) Date: Wed, 30 Aug 2023 15:05:07 +0000 Subject: [MINC-development] nonlinear .xfm for t1 (Kristi Drudik) In-Reply-To: References: Message-ID: Hi Claude, Thank you very much for your reply. Will play around with CIVET now. Best, Kristi -----Original Message----- From: minc-development-bounces at bic.mni.mcgill.ca On Behalf Of minc-development-request at bic.mni.mcgill.ca Sent: Tuesday, August 29, 2023 12:00 PM To: minc-development at bic.mni.mcgill.ca Subject: MINC-development Digest, Vol 86, Issue 1 [You don't often get email from minc-development-request at bic.mni.mcgill.ca. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Send MINC-development mailing list submissions to minc-development at bic.mni.mcgill.ca To subscribe or unsubscribe via the World Wide Web, visit https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development or, via email, send a message with subject or body 'help' to minc-development-request at bic.mni.mcgill.ca You can reach the person managing the list at minc-development-owner at bic.mni.mcgill.ca When replying, please edit your Subject line so it is more specific than "Re: Contents of MINC-development digest..." Today's Topics: 1. nonlinear .xfm for t1 (Kristi Drudik) 2. Re: nonlinear .xfm for t1 (Claude LEPAGE) ---------------------------------------------------------------------- Message: 1 Date: Mon, 28 Aug 2023 17:20:19 +0000 From: Kristi Drudik To: "minc-development at bic.mni.mcgill.ca" Subject: [MINC-development] nonlinear .xfm for t1 Message-ID: Content-Type: text/plain; charset="us-ascii" 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Mon, 28 Aug 2023 13:29:08 -0400 From: Claude LEPAGE 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 ------------------------------ Subject: Digest Footer _______________________________________________ MINC-development mailing list MINC-development at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development ------------------------------ End of MINC-development Digest, Vol 86, Issue 1 ***********************************************