Re: [caret-users] the name
Thank's Donna! On 13/03/07, Donna Dierker [EMAIL PROTECTED] wrote: Hi Ervin, I think the confusion stemmed from receiving a caret-users mailing list confirmation with a more personalized login and password around the same time you receive the download information. To download Caret, use this access information: To obtain the Caret software, use this login ID and password login: Rabbit password: Carrot Donna The Caret software can be downloaded from http://brainmap.wustl.edu/caret#DownloadCaret;. On 03/13/2007 08:01 AM, Ervin Berényi wrote: What is my name? The password is correct. I can't login to the downloading area. Ervin Berényi ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] About Monkey to Human Deformation
Dear David, In the Apply Deformation Map dialog box, I specified the following items: 1) Deformation Map File: the 23-LDMK deform_map file 2) File Type: Metric 3) Flat Max Edge Length: 10.00 4) Metric Deformation: Nearest Node (not sure which one is better?) 5) Smooth One Iteration (Except Flat) The other buttons were not clickable (the dialog box does not allow me to use them). When I click the Apply button, I immediately receive the following error message: Deform Error Is deformation map file valid? You must select a data file for deformation. You must select the output name for the deformed file. I tried to apply deformation map from two different .spec files: 1) Macaque F99 atlas directory, which has deformed metric files (from individual macaque to F99). I added/appended the .deform_map file to this .spec file before applying deformation. 2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06 directory). I added/appended my metric files to this .spec file before applying deformation. In both cases, I got the same error. Thanks for your helpful comments/suggestions, Reza Reza, On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote: Dear caret-users, David Van Essen suggested me to use the following .deform_map file for deformation of macaque F99 to Human PALS: RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23- LDMK-VE.73730.spec.deform_map Once you have a deform_map file, you can use it to register data sets from monkey to human WITHOUT re-running a registration. This is done using the Surface: Deformation: Apply Deformation Map option. If you want to register paint files, metric files, and most other files, you don't need anything other than the deform_map file to get the job done, and the dialog window is fairly self- explanatory. If you want to register a border projection file or a coordinate file, then you need additional coordinate and topology files that are available as part of the Caret Sept_06 tutorial dataset: http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595051archive_name=COMPARE_PALS_MacaqueF99.73730.spec The only reason to actually re-run an interspecies registration is IF you don't like the particular set of landmarks used and you want to try your own. If so, you should start with borderproj files also in: http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595051archive_name=COMPARE_PALS_MacaqueF99.73730.spec and make your additions and subtractions from there. See Part 4 of the latest Caret tutorial for more details on monkey- human comparisons. http://sumsdb.wustl.edu/sums/directory.do? id=6585200dir_name=CARET_TUTORIAL_SEPT-06 I specified this as my .deform_map file in the Spherical Parameters tab in the Spherical Surface Deformation dialog box. My question is what I should specify as .borderproj file. I have a borderproj file in my F99 directory (that I used for the registration of individual macaque to F99). I also have a borderproj file in my PALS directory (that I used for the registration of individual human to PALS). Should I use these borderproj files in the Individual and Atlas tabs in the Spherical Surface Deformation dialog box? Or there are other files that I should use? I also assume that the macaque F99 .spec file should be used in the Individual tab, and the human PALS .spec file should be used in the Atlas tab. See above. These steps should not be necessary for your purposes. I hope this helps. David Thanks for your help, Reza Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ 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 Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED]
Re: [caret-users] Announcement: open access MR data (OASIS)
In case it becomes useful to anyone, these 12 OASIS subjects comprise the PALS_B12: OAS1_0006_MR1 Human_Buckner_Case06 OAS1_0009_MR1 Human_Buckner_Case04 OAS1_0054_MR1 Human_Buckner_Case01 OAS1_0061_MR1 Human_Buckner_Case11 OAS1_0111_MR1 Human_Buckner_Case07 OAS1_0152_MR1 Human_Buckner_Case05 OAS1_0163_MR1 Human_Buckner_Case03 OAS1_0350_MR1 Human_Buckner_Case08 OAS1_0361_MR1 Human_Buckner_Case10 OAS1_0368_MR2 Human_Buckner_Case12 OAS1_0448_MR1 Human_Buckner_Case02 OAS1_0450_MR1 Human_Buckner_Case09 Donna Dierker http://brainmap.wustl.edu/ On 03/14/2007 12:37 PM, Daniel Marcus wrote: Dear Colleagues, The Open Access Series of Imaging Studies (OASIS) is now available at www.oasis-brains.org http://www.oasis-brains.org/. The data are publicly available under to a liberal Data Use Agreement available here: http://www.oasis-brains.org/app/template/UsageAgreement.vm. The first data set includes structural MR obtained from 416 subjects aged 18 to 96, including 100 subjects diagnosed with very mild to moderate Alzheimer’s Disease. A longitudinal data set will be released in the coming months. A manuscript describing the project is currently in press at Journal of Cognitive Neuroscience. For more information, please visit the website. Regards, Dan Marcus [EMAIL PROTECTED] Neuroinformatics Research Group Washington University School of Medicine http://nrg.wustl.edu http://nrg.wustl.edu/
[caret-users] Monkey Atlas and stereotaxic
Hi Caret-Gods...! I have a question regarding Caret and monkey atlas. I apologize for the basic nature of these questions, but I am a newbie to Caret and that is all i have to say in my defense!!! We have T1 weighted 0.5 isotropic resolution anatomical images of monkey brain. The final aim is to be able to reconstruct surfaces as well as find the co-ordinates of points of interest w.r.t our stereotaxic coord system. We are working with the inter-aural stereotaxic system. Ideally, apart from viewing the surface , we will need stereotaxic coordinates to know exactly where the AP0 is, mediolateral coordinates etc. I have ,as per the Caret segmentation tutorial, segmented the volume and created the surfaces. But, the way i have done it, the volume has been centered at the AC (as per the tutorial instructions). What should I do to center it to the inter-aural origin? is there any caret documentation on this... if yes, could you please point me to them? Consequently what would be the next steps I should perform (perhaps registration?) to be able to read off the stereo-coords of interest as per my coordinate system? Please do point me to the appropriate tutorials/spec files that i may need. Thanks in advance!! RN
Re: [caret-users] Monkey Atlas and stereotaxic
Hi Remya, Glad to hear you got your hands on a T1 scan. There's no documentation I know of that covers what you want to do, but it's not that hard (if I understand it correctly). I think you'll just need two versions of your volumes (one AC-centered, one inter-aural) and two versions of your fiducial surface (ditto). You'll need the AC-centered volume to create your fiducial surface, which also will be AC-centered. When you're happy with your AC-centered surface, then translate both volume and surface back to inter-aural. The hard part is calculating the x,y,z translation offsets between the AC-centered origin and your inter-aural origin. Sometimes it takes a sign flip or two to get it right, but only you can compute the magnitude of these shifts. I'll call them shiftx, shifty, shiftz. Change your volume back to inter-aural like so: Volume: Edit volume attributes: coordinates: origin: Adjust x,y,z by shiftx,shifty,shiftz. After applying change, hit toolbar: R (with volume view in main window) to reset the volume to the new origin, to make sure it's correct. This may take trial and error to get the sign right. Once the volume view accurately reflects the inter-aural origin, save the translated volume: File: Save Data File: volume files: NIFTI (or AFNI or SPM/MedX, which is basically Analyze): my_interaural.nii Now, translate your surface: * switch to fiducial view in main window * Window: Transformation matrix editor * Translate: enter shiftx, shifty, shiftz (again -- sign-flipping as needed) * Apply matrix to main window In this case, if you get it wrong, then you'll need to use Toolbar: spec to reload the fiducial after each trial, to get back to the original AC origin. Once you get it right, use File: Save data file: coord file to save the translated coord file as a name like my.fiducial.inter-aural.coord. Good luck. Donna On 03/14/2007 02:44 PM, Remya Nair wrote: Hi Caret-Gods...! I have a question regarding Caret and monkey atlas. I apologize for the basic nature of these questions, but I am a newbie to Caret and that is all i have to say in my defense!!! We have T1 weighted 0.5 isotropic resolution anatomical images of monkey brain. The final aim is to be able to reconstruct surfaces as well as find the co-ordinates of points of interest w.r.t our stereotaxic coord system. We are working with the inter-aural stereotaxic system. Ideally, apart from viewing the surface , we will need stereotaxic coordinates to know exactly where the AP0 is, mediolateral coordinates etc. I have ,as per the Caret segmentation tutorial, segmented the volume and created the surfaces. But, the way i have done it, the volume has been centered at the AC (as per the tutorial instructions). What should I do to center it to the inter-aural origin? is there any caret documentation on this... if yes, could you please point me to them? Consequently what would be the next steps I should perform (perhaps registration?) to be able to read off the stereo-coords of interest as per my coordinate system? Please do point me to the appropriate tutorials/spec files that i may need. Thanks in advance!! RN
