RE: [caret-users] Cortical Thickness Measurement
I am in the process of making the freesurfer surfaces for the scans so I can measure cortical thickness. After I finish that I want to import them into Caret. I wanted to see if there were any human specific steps in the script. As for the other question the goal is to look at differences across groups. I think I have a good starting point now. Thanks. -Eric -Original Message- From: Donna Dierker [mailto:[EMAIL PROTECTED] Sent: Wed 6/14/2006 8:41 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Cortical Thickness Measurement Hi Eric, I think I remember talking to you at NIH in February. First, let me clarify: Do you already have Freesurfer surfaces for these macaques? Or do you want to segment using Caret? If you already have Freesurfer surfaces, then the import script should still work for macaques. (The only iffy thing there might be the caret_command -volume-create parameters in the generate_depth part.) The general flattening and registration *procedures* are similar, but there are some important differences: 1. Registration target: There is no PALS for macaques -- at least not yet. (Some folks at Wash U are working on a multi-subject macaque atlas.) Meanwhile, we use our F99UA1 single subject macaque atlas as a registration target: Left: http://sumsdb.wustl.edu/sums/directory.do?dir_id=681250 Right: http://sumsdb.wustl.edu/sums/directory.do?dir_id=681256 2. Landmark set: Because macaques are so much less variable than humans in their folding patterns, you can count on more landmarks. The goals of your study dictate which landmarks are optimal. Do you want to optimize alignment of sulci/gyri across subjects, or look for anatomical differences across groups? On 06/13/2006 02:09 PM, Faden, Eric (NIH/NIMH) [F] wrote: 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=999719996view=cwchp=dGLbVzb-zSkzkmd5=0920fddff1134928d23f0a23d746935fie=/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
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=999719996view=cwchp=dGLbVzb-zSkzkmd5=0920fddff1134928d23f0a23d746935fie=/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
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=999719996view=cwchp=dGLbVzb-zSkzkmd5=0920fddff1134928d23f0a23d746935fie=/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
[caret-users] Macaque Segmentation
Hey All, Are there any special steps required outside of the standard tutorial for segmenting a Macaque brain? Or would the normal tutorial work correctly if followed? -Eric Faden
RE: [caret-users] Macaque Segmentation + AC/PC Align
I actually resampled them at .5mm already. The other problem I am having is that the way our monkeys are scanned they need to be rotated to the correct orientation (45 degrees or so). I tried to use the AC/PC align in Volume Attributes Editor. I selected the AC and PC then clicked align. After about 10 minutes I got a white cube where my volume used to be. Any thoughts on what this is? or what is a good way to AC/PC align my volume? -Eric -Original Message- From: Donna Dierker [mailto:[EMAIL PROTECTED] Sent: Wed 3/29/2006 10:58 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Macaque Segmentation The only difference that comes to mind is the voxdims. Resampling your macaque structural to cubic 0.5mm rather than cubic 1.0mm tends to work best (although I've seen 0.75mm work well). You definitely do NOT want to resample to cubic 1.0mm for monkeys. On 03/29/2006 09:53 AM, Faden, Eric (NIH/NIMH) [F] wrote: Hey All, Are there any special steps required outside of the standard tutorial for segmenting a Macaque brain? Or would the normal tutorial work correctly if followed? -Eric Faden ___ 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 winmail.dat
