[caret-users] Re: Mapping foci in Caret 5.5 using the Windows version
Hi, I use the Windows versions of Caret, and the foci mapping tools work fine for me, using both the 5.2 and 5.5 versions. Terry Sewards [EMAIL PROTECTED] wrote: Send caret-users mailing list submissions to caret-users@brainvis.wustl.edu To subscribe or unsubscribe via the World Wide Web, visit http://pulvinar.wustl.edu/mailman/listinfo/caret-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of caret-users digest... Today's Topics: 1. tutorial 5.2.2 mapping individual foci to the PALS atlas surface (J Labus) 2. Re: tutorial 5.2.2 mapping individual foci to the PALS atlas surface (David Vanessen) 3. [SPAM] Mapping Macaque SPM Functionals to aCaret Surface (Simone Kamphuis) 4. Re: Mapping Macaque SPM Functionals to a Caret Surface (Donna Dierker) 5. Re: Mapping Macaque SPM Functionals to a Caret Surface (Simone Kamphuis) -- Message: 1 Date: Mon, 06 Nov 2006 09:59:14 -0800 From: J Labus [EMAIL PROTECTED] Subject: [caret-users] tutorial 5.2.2 mapping individual foci to the PALSatlas surface To: caret-users@brainvis.wustl.edu Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=windows-1252; format=flowed I am flummoxed. I really like the looks of caret but have had no luck with past or present versions trying to do something which i expect should be easy for the program, namely map stereotaxic coordinates i from my own research onto the atlases. I have down loaded the newest version 5.5 along with tutorials and necessary spec files to attempt tutorial 5.2.2 but my efforts were unsuccessful. Has anyone tried this tutorial in Windows with success? As an aside: I found that the documentation doesn't quite follow the options that are given while performing the routine. For example, When i select the PALS_B12.BOTH.Test-STEREOTAXIC-FOCI.73730.spec the program is prompting me regarding overwriting the file or not and the documentation does not specify what to do. Is windows the wrong platform to be using? Does this platform have more bugs than say MAC OSX? As check, where do i find the spec files...i found them in the C:\Program Files\Caret\caret5_help\tutorials\CARET_TUTORIAL_SEPT06\MAPPING_PROCEDURES? The first scene that come up is not AVG Fiducial Dorsal...in fact this scene does not come up for me. Any direction would be appreciated.
Re: [caret-users] Mapping Macaque SPM Functionals to a Caret Surface
Dear Donna, It all worked out fine! The orientation of the anatomy and the functional volume was: anterior-posterior, left-right, inferior-superior. In SPM I changed this to LPI. Within SPM you can see the origin, which was -53, -65, -86 (you were almost right about them!) for the anatomy and -36, -52, -28 for the functional volume. I changed this back to 0 and that was all! The activation I find in SPM matches very nicely with the activation I see in Caret, so I am very happy about that. Thanks a lot! Simone Donna Dierker schrieb: Hi Simone, Actually, when I look at it in Caret, the functional and anatomical appear aligned, so that's good. When I use AFNI's to3d to create an AFNI .HEAD and .BRIK of rHerkules_1_18.hdr that specifies the orientation as ARI (anterior-to-posterior, right-to-left, inferior-to-superior), Caret flips it appropriately when opening. The attached capture before_translation.jpg shows that the orientation is good at least in the y and z planes, although I'm not sure about the x-flipping. (It might be left-to-right rather than right-to-left, as I asserted when using to3d.) But the origin is off, no doubt because you set the AC in Caret. The trick is finding the translation offset between the AC-centered and original volume. Using my own guess at the AC (-53,-65,-85) in Caret, I can get the volume and surface closer, but I suspect the x-flipping may still be wrong and the AC is probably still not set identically to your actual setting. I'm hoping you can take these clues and run with them on your own for a bit. Eventually, you'll need to either translate and flip your surface coordinate file (using AFNI's Vecwarp or Caret's Window: Transformation matrix editor) to match your volume file, or write your volume out with an orientation and origin that matches your surface. But first you need to get the magic numbers that specify the affine transform from your surface to your volume. On 11/07/2006 10:27 AM, Simone Kamphuis wrote: Donna Dierker schrieb: Hi Simone, In your case, your anatomical volume, functional volume, and surface are not aligned to one another. The anatomical is in a different orientation (and probably different origin) than the surface (which is LPI - http://brainmap.wustl.edu/SureFit/orient.html, as Caret expects it to be). The functional is in yet a different orientation. Step one is to get the anatomical and surface aligned, and then find some way to align the functional with the anatomical. This may require using some other software such as AFNI or SPM. If your anatomical and functional volume are in some different orientation, but there is an AFNI or NIfTI header that tells Caret what the orientation actually is, then Caret can flip it accordingly. But even if it gets the orientation right, there's still no guarantee the origins will align. Unfortunately, I'm real busy for the next three weeks, so I can't play around with them to figure it out on my own. See how far you can get on your end, and let me know tomorrow if you make no progress. On 11/07/2006 05:46 AM, Simone Kamphuis wrote: Dear Donna Dierker, I have read your answer to John Arsenault's e-mail. I also have problems to map functional data onto my monkey caret fiducial surface. I was wondering if you could have a look at the files that I used. (I will upload them to http://pulvinar.wustl.edu/cgi-bin/upload.cgi) I used CARET v5.3 (Jun 20 2005). Thank you in advance. Simone Materna ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users Dear Donna, I guess I should have send you my '..AC_left+orig.HEAD' file as well (I uploaded this file now). This file is in the same orientation as the surface. I used SPM to get the functional volume (T-map) in the same orientation as the anatomy (this might not seem to be the case at first sight, because the quality of the functional volume is not very good). I don't know how to get the anatomy (and functional volume) in the same orientation as the surface, since I can't open the '..AC_left+orig.HEAD' file in SPM. Thanks again, Simone ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Mapping Macaque SPM Functionals to a Caret Surface
I'm so glad. I'm never happy with almost perfectly aligned or eyeballing the alignment. I'm happy when I can figure out the magic numbers in a principled way. I'm even happier when users do it themselves, as you did. On 11/08/2006 10:16 AM, Simone Kamphuis wrote: Dear Donna, It all worked out fine! The orientation of the anatomy and the functional volume was: anterior-posterior, left-right, inferior-superior. In SPM I changed this to LPI. Within SPM you can see the origin, which was -53, -65, -86 (you were almost right about them!) for the anatomy and -36, -52, -28 for the functional volume. I changed this back to 0 and that was all! The activation I find in SPM matches very nicely with the activation I see in Caret, so I am very happy about that. Thanks a lot! Simone Donna Dierker schrieb: Hi Simone, Actually, when I look at it in Caret, the functional and anatomical appear aligned, so that's good. When I use AFNI's to3d to create an AFNI .HEAD and .BRIK of rHerkules_1_18.hdr that specifies the orientation as ARI (anterior-to-posterior, right-to-left, inferior-to-superior), Caret flips it appropriately when opening. The attached capture before_translation.jpg shows that the orientation is good at least in the y and z planes, although I'm not sure about the x-flipping. (It might be left-to-right rather than right-to-left, as I asserted when using to3d.) But the origin is off, no doubt because you set the AC in Caret. The trick is finding the translation offset between the AC-centered and original volume. Using my own guess at the AC (-53,-65,-85) in Caret, I can get the volume and surface closer, but I suspect the x-flipping may still be wrong and the AC is probably still not set identically to your actual setting. I'm hoping you can take these clues and run with them on your own for a bit. Eventually, you'll need to either translate and flip your surface coordinate file (using AFNI's Vecwarp or Caret's Window: Transformation matrix editor) to match your volume file, or write your volume out with an orientation and origin that matches your surface. But first you need to get the magic numbers that specify the affine transform from your surface to your volume. On 11/07/2006 10:27 AM, Simone Kamphuis wrote: Donna Dierker schrieb: Hi Simone, In your case, your anatomical volume, functional volume, and surface are not aligned to one another. The anatomical is in a different orientation (and probably different origin) than the surface (which is LPI - http://brainmap.wustl.edu/SureFit/orient.html, as Caret expects it to be). The functional is in yet a different orientation. Step one is to get the anatomical and surface aligned, and then find some way to align the functional with the anatomical. This may require using some other software such as AFNI or SPM. If your anatomical and functional volume are in some different orientation, but there is an AFNI or NIfTI header that tells Caret what the orientation actually is, then Caret can flip it accordingly. But even if it gets the orientation right, there's still no guarantee the origins will align. Unfortunately, I'm real busy for the next three weeks, so I can't play around with them to figure it out on my own. See how far you can get on your end, and let me know tomorrow if you make no progress. On 11/07/2006 05:46 AM, Simone Kamphuis wrote: Dear Donna Dierker, I have read your answer to John Arsenault's e-mail. I also have problems to map functional data onto my monkey caret fiducial surface. I was wondering if you could have a look at the files that I used. (I will upload them to http://pulvinar.wustl.edu/cgi-bin/upload.cgi) I used CARET v5.3 (Jun 20 2005). Thank you in advance. Simone Materna ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users Dear Donna, I guess I should have send you my '..AC_left+orig.HEAD' file as well (I uploaded this file now). This file is in the same orientation as the surface. I used SPM to get the functional volume (T-map) in the same orientation as the anatomy (this might not seem to be the case at first sight, because the quality of the functional volume is not very good). I don't know how to get the anatomy (and functional volume) in the same orientation as the surface, since I can't open the '..AC_left+orig.HEAD' file in SPM. Thanks again, Simone ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu
[caret-users] registration landmarks
Hi, I have attached a screen capture of the flat map, inflated map and spherical map with the 3 additional registration landmarks drawn. The flat map appears a bit more distorted than I am used to seeing and the sylvian fissure shape also seems atypical. I wanted to get a sanity check on the flat map and make sure I am not missing anything and constructive feedback on how my landmark borders look before moving forward. Thanks in advance for your feedback, Veronica attachment: flatmap.jpgattachment: sphere1.jpgattachment: sphere2.jpgattachment: veryinflated.jpg
Re: [caret-users] registration landmarks
On 11/08/2006 01:39 PM, Veronica S Smith wrote: Hi, I have attached a screen capture of the flat map, inflated map and spherical map with the 3 additional registration landmarks drawn. Yeah, there are a lot of crossovers in the flat map near the sylvian, but they don't seem to have interfered with your drawing the sylvian border. On the other hand, what looks like some folding over in the central sulcus is causing an undesirable zig-zag (or S shape between the middle and dorsal ends of the CeS) in that border. Perhaps some judicious border point trimming may allow you to sidestep this problem, Moving border points will be tricky, because you can do that only on a flat map, and it looks like you have problems with the CeS creasing over in that region (i.e., what led to the zig-zag in the first place). The flat map appears a bit more distorted than I am used to seeing and the sylvian fissure shape also seems atypical. The flat map is borderline disaster, but unless you're using it for more than a tool to draw your registration borders, or it prevents you from drawing decent registration borders, I wouldn't worry about it. If need be, you may be able to draw draw your CeS border on the very inflated surface (making sure you switch from 2D to 3D mode). But I think I'd try deleting some points to rectify the zig-zag and see how that works. To really judge your sylvian, we'd need the dataset. Just eyeballing these captures, it does look a little weird, but it seems to be reflecting the anatomy reasonably well. Your anterior termination looks too far superior and posterior -- roughly 15-30 degrees too far clockwise. Can't just the posterior end without the dataset, but it looks reasonable. I wanted to get a sanity check on the flat map and make sure I am not missing anything and constructive feedback on how my landmark borders look before moving forward. Thanks in advance for your feedback, Veronica -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
Re: [caret-users] registration landmarks
On 11/08/2006 02:12 PM, Donna Dierker wrote: Your anterior termination looks too far superior and posterior -- roughly 15-30 degrees too far clockwise. I should have specified when looking at the lateral inflated view.
