Re: [caret-users] Spherical registration
Hi Donna, I don't know what happened, but now all the links work. Thanks, Mateus Donna Dierker wrote: Mateus, Yes -- that's the right archive. I don't understand why you're getting the time out errors; I can't replicate the problem on my end. What happens when you try this link (i.e., same, except port number omitted): http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499 On 11/28/2006 01:03 PM, Mateus Joffily wrote: Hi Donna, I don't know if I am the only one experiencing this problem, but I am also unable to access the location: http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499. I still get a 'time out error'. However, I can access the SuMS database from http://sumsdb.wustl.edu/. Could you, please, confirm me if this is the atlas that I need to download: 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730'? Thanks, Mateus Donna Dierker wrote: On 11/28/2006 11:48 AM, Mateus Joffily wrote: Hi, I am a little bit confused on how to proceed to register an individual surface into an Atlas. The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' explains how to perform a spherical registration using the 'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My questions are: 1) What spec file should I use to register into the right hemisphere? 2) If I choose to register into PALS-B12 atlas, what files should I use? The answer to both 1) and 2) is use the PALS_B12 LR combo registration target dataset: http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499 And use the template deform_map included in that dataset to preset your registration parameters. See this page and Erin's cheat sheet (linked from the page below) for more details: http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html This is what we do. There are separate landmark datasets for the left and right, but they differ very little, and using the LR combo enables you to do cross-hem or inter-hem analyses. The way we look at it, there's very little down side to using the combo dataset, but a lot of up side to doing so. So we routinely use the LR combo now. We stopped using colin as a registration target a couple of years ago, but some documentation may still refer to it. Thanks, Mateus ___ 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 http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Spherical registration
I did remove the port numbers from the list, which seemed to have no ill effect on my end. Perhaps it resolved the problem on your end. On 11/29/2006 03:15 AM, Mateus Joffily wrote: Hi Donna, I don't know what happened, but now all the links work. Thanks, Mateus Donna Dierker wrote: Mateus, Yes -- that's the right archive. I don't understand why you're getting the time out errors; I can't replicate the problem on my end. What happens when you try this link (i.e., same, except port number omitted): http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499 On 11/28/2006 01:03 PM, Mateus Joffily wrote: Hi Donna, I don't know if I am the only one experiencing this problem, but I am also unable to access the location: http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499. I still get a 'time out error'. However, I can access the SuMS database from http://sumsdb.wustl.edu/. Could you, please, confirm me if this is the atlas that I need to download: 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730'? Thanks, Mateus Donna Dierker wrote: On 11/28/2006 11:48 AM, Mateus Joffily wrote: Hi, I am a little bit confused on how to proceed to register an individual surface into an Atlas. The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' explains how to perform a spherical registration using the 'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My questions are: 1) What spec file should I use to register into the right hemisphere? 2) If I choose to register into PALS-B12 atlas, what files should I use? The answer to both 1) and 2) is use the PALS_B12 LR combo registration target dataset: http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499 And use the template deform_map included in that dataset to preset your registration parameters. See this page and Erin's cheat sheet (linked from the page below) for more details: http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html This is what we do. There are separate landmark datasets for the left and right, but they differ very little, and using the LR combo enables you to do cross-hem or inter-hem analyses. The way we look at it, there's very little down side to using the combo dataset, but a lot of up side to doing so. So we routinely use the LR combo now. We stopped using colin as a registration target a couple of years ago, but some documentation may still refer to it. Thanks, Mateus ___ 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 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 -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
[caret-users] border color file
Hi Donna, When I try to load the border files, after the surface alignement, I get the warning message: 'You have selected border files that require a border color file but no border color file is selected'. In Erin's document, it is said to: File : Open Data File : File Type = Border Color Files - Find ‘ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor’ - Yes – Copy to current directory But, I can't find this file anywhere. Do you know where it is saved? Is it 'Human.TEMPLATE-CUTS_STANDARD.03-05.bordercolor'? Thanks again for your help. Mateus
Re: [caret-users] border color file
Hi Mateus, You can find the border color file in the PALS_B12.LR directory. Erin Mateus Joffily wrote: Hi Donna, When I try to load the border files, after the surface alignement, I get the warning message: 'You have selected border files that require a border color file but no border color file is selected'. In Erin's document, it is said to: File : Open Data File : File Type = Border Color Files - Find ‘ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor’ - Yes – Copy to current directory But, I can't find this file anywhere. Do you know where it is saved? Is it 'Human.TEMPLATE-CUTS_STANDARD.03-05.bordercolor'? Thanks again for your help. Mateus ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
[caret-users] crash of X KDE session
Hi Donna and Hohn, I am experiencing a severe problem with my caret installation in linux: whenever I try to import an Analyze Volume file, my entire X session immediately crashes, including all applications and I have to login in KDE from scratch. I couldn't tell whether the problem is limited to the Import function only, because the system crashes so badly that I thought it would be better to obtain some feedback from you before doing some debugging. But all the other display functions of caret that I have tried out (rendering surfaces, overlaying metric maps and so on) seem to work fine. I first encountered the problem a few days ago. I completely ignore what could be the origin of the problem. I had used the same installation without any problems before, including the Import function. I have also tried to do a fresh install, of both versions 5.4 and 5.5, but the problem persists. I did some updates of KDE and xorg recently, though, and I suspect that the problem may have arosen since then. All other applications run fine, though. Also, I have installed the same .zip caret tar ball on another machine and there it runs fine... This is the kernel of my machine: Linux bll4 2.6.11-kanotix-11 #1 Sun May 29 22:32:10 CEST 2005 i686 GNU/Linux Any help would be greatly appreciated! Best, Marco -- Marco Tettamanti, Ph.D. San Raffaele Scientific Institute Facoltà di Psicologia Via Olgettina 58 I-20132 Milano, Italy Tel. ++39-02-26434888 Fax ++39-02-26434892 Email: [EMAIL PROTECTED]
Re: [caret-users] crash of X KDE session
Marco, Another user had a problem similar to this. I believe it has to do with the FreeType library which gets used to create text characters that are drawn on the volume slices to show the voxel and its stereotaxic coordinate. See if there is a file in your home directory named .fonts.conf (note that the file begins with a period so use the command ls -a to see the file). If .fonts.conf exists, rename it, start Caret, and see if you can import a volume. For more info: http://www.mail-archive.com/caret- [EMAIL PROTECTED]/msg00892.html -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Nov 29, 2006, at 10:42 AM, marco tettamanti wrote: Hi Donna and Hohn, I am experiencing a severe problem with my caret installation in linux: whenever I try to import an Analyze Volume file, my entire X session immediately crashes, including all applications and I have to login in KDE from scratch. I couldn't tell whether the problem is limited to the Import function only, because the system crashes so badly that I thought it would be better to obtain some feedback from you before doing some debugging. But all the other display functions of caret that I have tried out (rendering surfaces, overlaying metric maps and so on) seem to work fine. I first encountered the problem a few days ago. I completely ignore what could be the origin of the problem. I had used the same installation without any problems before, including the Import function. I have also tried to do a fresh install, of both versions 5.4 and 5.5, but the problem persists. I did some updates of KDE and xorg recently, though, and I suspect that the problem may have arosen since then. All other applications run fine, though. Also, I have installed the same .zip caret tar ball on another machine and there it runs fine... This is the kernel of my machine: Linux bll4 2.6.11-kanotix-11 #1 Sun May 29 22:32:10 CEST 2005 i686 GNU/Linux Any help would be greatly appreciated! Best, Marco -- Marco Tettamanti, Ph.D. San Raffaele Scientific Institute Facoltà di Psicologia Via Olgettina 58 I-20132 Milano, Italy Tel. ++39-02-26434888 Fax ++39-02-26434892 Email: [EMAIL PROTECTED] ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] distance from a node
If you were talking about geodesic distance (i.e., running along the contour of the fiducial surface -- not as the crow flies through the CSF/WM), then you could use the Surface: ROI feature for this purpose. (First operation Geodesic Distance, and then threshold the resulting metric at the desired distance.) I'm not aware of something like that for 3D distances, but there's a Make Sphere feature in Window: Script Builder. Worst case, you could generate a sphere around the enclosing voxel and map that ROI volume to the surface. On 11/29/2006 11:18 AM, Mateus Joffily wrote: Hi, In Caret5.5, is there a way of selecting a node and finding all (or some) nodes that are at a given distance from it? I think I am looking for something similar to what is described in section 2.17.2 (Foci Data Searches) of the 'Caret Tutorial – the Basics'. But Section 2.17.2 regards only WebCaret. Does it exist something similar to Caret5.5? Thanks, Mateus ___ 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] crash of X KDE session
Hi Marco, Although your problem is a bit different, another possible culprit is the .caret5_preferences file: http://brainvis.wustl.edu/pipermail/caret-users/2006-November/000931.html We're still struggling with this problem at University of Washington. Today I asked Veronica to try the attached script, which strips the recent files and directories from the caret preferences before launching caret. I'm curious whether it helps in your case, in case the .fonts.conf trick fails. Let us know what you find. On 11/29/2006 11:19 AM, John Harwell wrote: Marco, Another user had a problem similar to this. I believe it has to do with the FreeType library which gets used to create text characters that are drawn on the volume slices to show the voxel and its stereotaxic coordinate. See if there is a file in your home directory named .fonts.conf (note that the file begins with a period so use the command ls -a to see the file). If .fonts.conf exists, rename it, start Caret, and see if you can import a volume. For more info: http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00892.html -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Nov 29, 2006, at 10:42 AM, marco tettamanti wrote: Hi Donna and Hohn, I am experiencing a severe problem with my caret installation in linux: whenever I try to import an Analyze Volume file, my entire X session immediately crashes, including all applications and I have to login in KDE from scratch. I couldn't tell whether the problem is limited to the Import function only, because the system crashes so badly that I thought it would be better to obtain some feedback from you before doing some debugging. But all the other display functions of caret that I have tried out (rendering surfaces, overlaying metric maps and so on) seem to work fine. I first encountered the problem a few days ago. I completely ignore what could be the origin of the problem. I had used the same installation without any problems before, including the Import function. I have also tried to do a fresh install, of both versions 5.4 and 5.5, but the problem persists. I did some updates of KDE and xorg recently, though, and I suspect that the problem may have arosen since then. All other applications run fine, though. Also, I have installed the same .zip caret tar ball on another machine and there it runs fine... This is the kernel of my machine: Linux bll4 2.6.11-kanotix-11 #1 Sun May 29 22:32:10 CEST 2005 i686 GNU/Linux Any help would be greatly appreciated! Best, Marco --Marco Tettamanti, Ph.D. San Raffaele Scientific Institute Facoltà di Psicologia Via Olgettina 58 I-20132 Milano, Italy Tel. ++39-02-26434888 Fax ++39-02-26434892 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 -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) caret_prefs_stripper.sh Description: Bourne shell script
