RE: [caret-users] Cortical Thickness Measurement
I suppose I should have been more specific. Is there any Macaque specific information? -Eric -Original Message- From: Donna Dierker [mailto:[EMAIL PROTECTED] Sent: Tue 6/13/2006 2:48 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Cortical Thickness Measurement Hi Eric, We haven't updated the old Freesurfer-to-Caret tutorial, but you might find these caret-users posts helpful: http://brainvis.wustl.edu/pipermail/caret-users/2006-February/000686.html http://brainvis.wustl.edu/pipermail/caret-users/2006-February/000687.html Entering caret_command -help at the command line will spew 954 lines of helpful text, as well. If these don't cover what you want to do, post back here and we'll see if we can help. On 06/13/2006 08:31 AM, Faden, Eric (NIH/NIMH) [F] wrote: >Are there instructions somewhere for importing from FreeSurfer to Caret 5.4 >somewhere? The only instructions seem to be fairly old and it looks like >things have changed a bit since then. > >-Eric > >-Original Message- >From: Donna Dierker [mailto:[EMAIL PROTECTED] >Sent: Tue 6/13/2006 8:36 AM >To: [EMAIL PROTECTED]; Caret, SureFit,and SuMS software users >Subject: Re: [caret-users] Cortical Thickness Measurement > >Hi Darren, > >Sorry to be the bearer of bad news, but no: Caret/SureFit doesn't >compute cortical thickness. For a while, a student was working on it, >but it never went anywhere. Occasionally, people mistake our sulcal >depth measure for cortical thickness, but the two are completely >different measures. (See David's PALS paper >(http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WNP-4H4T34K-1-3&_cdi=6968&_user=4275&_orig=browse&_coverDate=11%2F15%2F2005&_sk=999719996&view=c&wchp=dGLbVzb-zSkzk&md5=0920fddff1134928d23f0a23d746935f&ie=/sdarticle.pdf), > >figure 1, for a description of sulcal depth.) > >The only good news I can give those who are interested in cortical >thickness is that you can import your freesurfer surfaces and thickness >maps into Caret in a mostly automated way, and generate sulcal depth on >them, if desired. You can then register them to the PALS_B12 atlas, >although this requires drawing our Core6 landmark borders: > >http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html > >Due to algorithmic differences between Freesurfer's and Caret's >registration algorithms, seeking a "second opinion" can be useful, >depending on the nature of your study. For example, the algorithm that >best aligns intrasubject anatomy across multiple timepoints may not be >ideal for finding group anatomical differences. > >On 06/12/2006 09:09 PM, Darren Weber wrote: > > > >>-BEGIN PGP SIGNED MESSAGE- >>Hash: SHA1 >> >> >>Hi, >> >>I have been using FreeSurfer for a while, to obtain cortical thickness >>measures. Is it now possible to obtain thickness measures with caret? >> >>There is a previous thread from 2003 indicating this feature was on a >>wish-list: >> >>http://brainvis.wustl.edu/pipermail/caret-users/2003-September/76.html >> >> >>Thanks, Darren >> >> >>- -- >> >>Darren L. Weber, Ph.D. >>Postdoctoral Scholar >> >>Dynamic Neuroimaging Laboratory, >>UCSF Department of Radiology, >>185 Berry Street, Suite 350, Box 0946, >>San Francisco, CA 94107, USA. >> >>Tel: +1 415 353-9444 >>Fax: +1 415 353-9421 >>www: http://dnl.ucsf.edu/users/dweber >> >>"To explicate the uses of the brain seems as difficult >>a task as to paint the soul, of which it is commonly >>said, that it understands all things but itself." >> Thomas Willis (The Anatomy of the Brain and Nerves, 1664) >>-BEGIN PGP SIGNATURE- >>Version: GnuPG v1.4.3 (GNU/Linux) >>Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org >> >>iD8DBQFEjh5kxaCYN7qs0v4RAh7lAJ93FoghevMObd2n4idytpsuYLxoJQCeOdKY >>/817YAHiHOSBRPgzJbB1IJI= >>=/WHa >>-END PGP SIGNATURE- >> >>___ >>caret-users mailing list >>caret-users@brainvis.wustl.edu >>http://pulvinar.wustl.edu/mailman/listinfo/caret-users >> >> >> >> >> > > > > -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Cortical Thickness Measurement
Hi Eric, We haven't updated the old Freesurfer-to-Caret tutorial, but you might find these caret-users posts helpful: http://brainvis.wustl.edu/pipermail/caret-users/2006-February/000686.html http://brainvis.wustl.edu/pipermail/caret-users/2006-February/000687.html Entering caret_command -help at the command line will spew 954 lines of helpful text, as well. If these don't cover what you want to do, post back here and we'll see if we can help. On 06/13/2006 08:31 AM, Faden, Eric (NIH/NIMH) [F] wrote: Are there instructions somewhere for importing from FreeSurfer to Caret 5.4 somewhere? The only instructions seem to be fairly old and it looks like things have changed a bit since then. -Eric -Original Message- From: Donna Dierker [mailto:[EMAIL PROTECTED] Sent: Tue 6/13/2006 8:36 AM To: [EMAIL PROTECTED]; Caret, SureFit,and SuMS software users Subject: Re: [caret-users] Cortical Thickness Measurement Hi Darren, Sorry to be the bearer of bad news, but no: Caret/SureFit doesn't compute cortical thickness. For a while, a student was working on it, but it never went anywhere. Occasionally, people mistake our sulcal depth measure for cortical thickness, but the two are completely different measures. (See David's PALS paper (http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WNP-4H4T34K-1-3&_cdi=6968&_user=4275&_orig=browse&_coverDate=11%2F15%2F2005&_sk=999719996&view=c&wchp=dGLbVzb-zSkzk&md5=0920fddff1134928d23f0a23d746935f&ie=/sdarticle.pdf), figure 1, for a description of sulcal depth.) The only good news I can give those who are interested in cortical thickness is that you can import your freesurfer surfaces and thickness maps into Caret in a mostly automated way, and generate sulcal depth on them, if desired. You can then register them to the PALS_B12 atlas, although this requires drawing our Core6 landmark borders: http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html Due to algorithmic differences between Freesurfer's and Caret's registration algorithms, seeking a "second opinion" can be useful, depending on the nature of your study. For example, the algorithm that best aligns intrasubject anatomy across multiple timepoints may not be ideal for finding group anatomical differences. On 06/12/2006 09:09 PM, Darren Weber wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, I have been using FreeSurfer for a while, to obtain cortical thickness measures. Is it now possible to obtain thickness measures with caret? There is a previous thread from 2003 indicating this feature was on a wish-list: http://brainvis.wustl.edu/pipermail/caret-users/2003-September/76.html Thanks, Darren - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.3 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFEjh5kxaCYN7qs0v4RAh7lAJ93FoghevMObd2n4idytpsuYLxoJQCeOdKY /817YAHiHOSBRPgzJbB1IJI= =/WHa -END PGP SIGNATURE- ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
RE: [caret-users] Cortical Thickness Measurement
Are there instructions somewhere for importing from FreeSurfer to Caret 5.4 somewhere? The only instructions seem to be fairly old and it looks like things have changed a bit since then. -Eric -Original Message- From: Donna Dierker [mailto:[EMAIL PROTECTED] Sent: Tue 6/13/2006 8:36 AM To: [EMAIL PROTECTED]; Caret, SureFit,and SuMS software users Subject: Re: [caret-users] Cortical Thickness Measurement Hi Darren, Sorry to be the bearer of bad news, but no: Caret/SureFit doesn't compute cortical thickness. For a while, a student was working on it, but it never went anywhere. Occasionally, people mistake our sulcal depth measure for cortical thickness, but the two are completely different measures. (See David's PALS paper (http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WNP-4H4T34K-1-3&_cdi=6968&_user=4275&_orig=browse&_coverDate=11%2F15%2F2005&_sk=999719996&view=c&wchp=dGLbVzb-zSkzk&md5=0920fddff1134928d23f0a23d746935f&ie=/sdarticle.pdf), figure 1, for a description of sulcal depth.) The only good news I can give those who are interested in cortical thickness is that you can import your freesurfer surfaces and thickness maps into Caret in a mostly automated way, and generate sulcal depth on them, if desired. You can then register them to the PALS_B12 atlas, although this requires drawing our Core6 landmark borders: http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html Due to algorithmic differences between Freesurfer's and Caret's registration algorithms, seeking a "second opinion" can be useful, depending on the nature of your study. For example, the algorithm that best aligns intrasubject anatomy across multiple timepoints may not be ideal for finding group anatomical differences. On 06/12/2006 09:09 PM, Darren Weber wrote: >-BEGIN PGP SIGNED MESSAGE- >Hash: SHA1 > > >Hi, > >I have been using FreeSurfer for a while, to obtain cortical thickness >measures. Is it now possible to obtain thickness measures with caret? > >There is a previous thread from 2003 indicating this feature was on a >wish-list: > >http://brainvis.wustl.edu/pipermail/caret-users/2003-September/76.html > > >Thanks, Darren > > >- -- > >Darren L. Weber, Ph.D. >Postdoctoral Scholar > >Dynamic Neuroimaging Laboratory, >UCSF Department of Radiology, >185 Berry Street, Suite 350, Box 0946, >San Francisco, CA 94107, USA. > >Tel: +1 415 353-9444 >Fax: +1 415 353-9421 >www: http://dnl.ucsf.edu/users/dweber > >"To explicate the uses of the brain seems as difficult >a task as to paint the soul, of which it is commonly >said, that it understands all things but itself." > Thomas Willis (The Anatomy of the Brain and Nerves, 1664) >-BEGIN PGP SIGNATURE- >Version: GnuPG v1.4.3 (GNU/Linux) >Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > >iD8DBQFEjh5kxaCYN7qs0v4RAh7lAJ93FoghevMObd2n4idytpsuYLxoJQCeOdKY >/817YAHiHOSBRPgzJbB1IJI= >=/WHa >-END PGP SIGNATURE- > >___ >caret-users mailing list >caret-users@brainvis.wustl.edu >http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Cortical Thickness Measurement
Hi Darren, Sorry to be the bearer of bad news, but no: Caret/SureFit doesn't compute cortical thickness. For a while, a student was working on it, but it never went anywhere. Occasionally, people mistake our sulcal depth measure for cortical thickness, but the two are completely different measures. (See David's PALS paper (http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WNP-4H4T34K-1-3&_cdi=6968&_user=4275&_orig=browse&_coverDate=11%2F15%2F2005&_sk=999719996&view=c&wchp=dGLbVzb-zSkzk&md5=0920fddff1134928d23f0a23d746935f&ie=/sdarticle.pdf), figure 1, for a description of sulcal depth.) The only good news I can give those who are interested in cortical thickness is that you can import your freesurfer surfaces and thickness maps into Caret in a mostly automated way, and generate sulcal depth on them, if desired. You can then register them to the PALS_B12 atlas, although this requires drawing our Core6 landmark borders: http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html Due to algorithmic differences between Freesurfer's and Caret's registration algorithms, seeking a "second opinion" can be useful, depending on the nature of your study. For example, the algorithm that best aligns intrasubject anatomy across multiple timepoints may not be ideal for finding group anatomical differences. On 06/12/2006 09:09 PM, Darren Weber wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, I have been using FreeSurfer for a while, to obtain cortical thickness measures. Is it now possible to obtain thickness measures with caret? There is a previous thread from 2003 indicating this feature was on a wish-list: http://brainvis.wustl.edu/pipermail/caret-users/2003-September/76.html Thanks, Darren - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.3 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFEjh5kxaCYN7qs0v4RAh7lAJ93FoghevMObd2n4idytpsuYLxoJQCeOdKY /817YAHiHOSBRPgzJbB1IJI= =/WHa -END PGP SIGNATURE- ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
