Re: [caret-users] crash of X KDE session
Hi John and Donna, I tried both of your methods, but unfortunately none solved my problem... I have tried to rename the file .fonts.conf, alone and, following the thread between Roland and you, together with .fonts.cache-1 and .fontconfig/ I also tried running Donna's script sh ./caret_prefs_stripper.sh. Helas, my entire X session always crashes when I import an Analyze image file. My problem seem to be different form Roland's and Veronica's ones, in that the problem is not limited to Caret, but it affects the entire X environment. Best, Marco 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 -- 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] distance from a node
Hi David, Thanks for your reply. I asked for this capability because I am trying to perform a spherical registration. Many landmarks are defined as starting and terminating at a certain distance from an anatomical reference point. I thought that a tool, which allows the user to enter a reference point coordinate in the surface and, after, displays every node that is at a given geodesic distance from it, would be helpful This capability is not essential for me. I was wondering if it was already implemented in Caret. Best regards, Mateus David Vanessen wrote: Mateus, First, it is important to clarify whether your request pertains to nodes (as stated) or to foci. In Caret terminology, nodes refers specifically to the points that make up a surface and have locations specified within a coordinate file. Foci refers to stereotaxically identified locations (typically fMRI activation centers) that are specified within a foci file or foci projection file. I'm guessing you are referring to foci, but let us know. At present, I don't think that the capability you are asking about exists for either nodes or foci. If you can let us know what you will be using this for and whether this is a pressing need, it will help us to prioritize the request. Also, if other Caret users would like to see this functionality, let us know. Best regards, David On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote: 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.) ___ 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] projecting PALS-B12 atlas into individual brain
Hi, I have concluded the spherical registration of one individual surface into PALS-B12. Three spec files have been created: (1) Human.Isa.R.spec (original spec file); (2) deformed_Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec; (3) deformed_Human.Isa.R.spec; Could you, please, precise me differences among those three specs and for what purpose should I use each one? Although the names seem to be informative, when I compare the surfaces linked to each one, they look very similar, if not the same. In the next step, I would like to project PALS_B12 atlas (borders and paints) into the non-deformed individual surface. Could you, please, point me the documentation that explains how to do that, and how do I use the deformation map files? Thanks again for your help. Mateus
Re: [caret-users] Spherical registration
Hi, In the 'Caret5 Tutorial', during the spherical registration procedure, it is instructed to use the 'Human to Human' standard parameters (in Surface: Deformation: Run Spherical Surface Deformation: Spherical Parameters: Set Parameters). However, in Erin's cheat sheet, it is instructed to read params from: Def Map File: 'TEMPLATE_REG-with-POP-AVG_4k_NoFid.deform_map'. If I am using 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730' atlas, which procedure should I follow? Thanks, Mateus Donna Dierker wrote: 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
Re: [caret-users] distance from a node
Oh! That's ridiculously easy. Those reference distances are in mm on the inflated (except for the staring sylvian, which is relative to the flat surface). You click one node on, say, the occipital pole; then you click a border point along the calcarine you guesstimate is about 24mm from the occipital pole; and you read out the Distance on the ID window. This is a 3D distance (make sure you read the Inflated surface's distance, or flat if sylvian). If your occipital pole point is offset significantly from the border point along the x or z axes, then use the Y component of the respective points and compute the difference. For example, there's a pretty big x and z offset between this occipital pole (first) and candidate most-posterior calcarine border point: Node 20734 Main Window Inflated XYZ: 15.015987396, -110.156700134, -22.251829147 Shape: -2.904558420 -2.124466896 Node 32819 Main Window Inflated XYZ: 27.664737701, -77.988800049, -6.281192303 Distance: 38.076580048 Shape: -10.455765724 -8.209010124 So I compute -110 - -78 = 32 -- so this point is 32mm from the occipital pole, so we need to find one whose y component of the inflated coordinate is closer to like -110 + 24 = -86. Hope this helps! On 11/30/2006 06:53 AM, Mateus Joffily wrote: Hi David, Thanks for your reply. I asked for this capability because I am trying to perform a spherical registration. Many landmarks are defined as starting and terminating at a certain distance from an anatomical reference point. I thought that a tool, which allows the user to enter a reference point coordinate in the surface and, after, displays every node that is at a given geodesic distance from it, would be helpful This capability is not essential for me. I was wondering if it was already implemented in Caret. Best regards, Mateus David Vanessen wrote: Mateus, First, it is important to clarify whether your request pertains to nodes (as stated) or to foci. In Caret terminology, nodes refers specifically to the points that make up a surface and have locations specified within a coordinate file. Foci refers to stereotaxically identified locations (typically fMRI activation centers) that are specified within a foci file or foci projection file. I'm guessing you are referring to foci, but let us know. At present, I don't think that the capability you are asking about exists for either nodes or foci. If you can let us know what you will be using this for and whether this is a pressing need, it will help us to prioritize the request. Also, if other Caret users would like to see this functionality, let us know. Best regards, David On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote: 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.) ___ 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.)
Re: [caret-users] crash of X KDE session
Marco, Does the problem occur when you use File: Open Volume Anatomy (or functional) File to open the same file? If so, does it occur if you convert the file to NIfTI and/or AFNI? I'm guessing it will (e.g., suggesting a display issue, rather than a file I/O issue), but it helps to be sure. If you have trouble converting to another file format, then upload the file here, and I'll provide you the converted version: http://pulvinar.wustl.edu/cgi-bin/upload.cgi On 11/30/2006 04:08 AM, marco tettamanti wrote: Hi John and Donna, I tried both of your methods, but unfortunately none solved my problem... I have tried to rename the file .fonts.conf, alone and, following the thread between Roland and you, together with .fonts.cache-1 and .fontconfig/ I also tried running Donna's script sh ./caret_prefs_stripper.sh. Helas, my entire X session always crashes when I import an Analyze image file. My problem seem to be different form Roland's and Veronica's ones, in that the problem is not limited to Caret, but it affects the entire X environment. Best, Marco 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.)
Re: [caret-users] projecting PALS-B12 atlas into individual brain
On 11/30/2006 08:34 AM, Mateus Joffily wrote: Hi, I have concluded the spherical registration of one individual surface into PALS-B12. Three spec files have been created: (1) Human.Isa.R.spec (original spec file); (2) deformed_Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec; (3) deformed_Human.Isa.R.spec; Could you, please, precise me differences among those three specs and for what purpose should I use each one? Although the names seem to be informative, when I compare the surfaces linked to each one, they look very similar, if not the same. 1) The original is what you created during segmentation, flattening, etc. 2) The deformed_Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec should be in your individual's surface directory. The dataset you downloaded is a stripped down version that contains no goodies (e.g., PALS border and paints, which you cite below). To get such goodies to automagically deform to your subjects' directories when you run registration, put the goodies in the atlas target directory and add them to your target registration spec (i.e., Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec). The one you currently have offers little, since it's designed more for the individual - atlas direction (e.g., getting a bunch of depth or fMRI maps on the PALS mesh). But in your case, you care more about atlas - individual. 3) The deformed_Human.Isa.R.spec is in your atlas target directory. Other than sanity checking the deformed fiducial, I don't personally use this spec file much. (And even when sanity checking, I use a SANITY_CHECK.spec that includes ALL my deformed fiducials and a single PALS closed topo.) More typically, you're interested in a particular file type -- e.g., deformed surface shape for sulcal depth; deformed metric for fMRI; deformed fiducial coord file for average fiducials. One typically concatenates all the deformed shape/metric into composite files and does group statistics on them. In the next step, I would like to project PALS_B12 atlas (borders and paints) into the non-deformed individual surface. Could you, please, point me the documentation that explains how to do that, and how do I use the deformation map files? The hard part is figuring out exactly which goodies (e.g., PALS paint, border, metric) you want deformed. Search for them in sumsdb.wustl.edu, or more likely find them in existing tutorials or datasets from figures in published papers that cite sumsdb links. You may find that the goodies in the visualization specs off the landmarks page meet your needs. If so, copy the appropriate paint, areacolor, border, bordercolor, metric, and/or palette files to your atlas target directory. Then add them to your atlas target spec. Then either re-run any registrations, or use Surface: Deformation: apply deformation map to apply the map in your individual's surface directory to the files in your atlas target directory. Thanks again for your help. Mateus -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
Re: [caret-users] Spherical registration
Here is the pecking order (believe in this order): Landmark page (http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html) Cheat sheet Tutorial On 11/30/2006 09:00 AM, Mateus Joffily wrote: Hi, In the 'Caret5 Tutorial', during the spherical registration procedure, it is instructed to use the 'Human to Human' standard parameters (in Surface: Deformation: Run Spherical Surface Deformation: Spherical Parameters: Set Parameters). However, in Erin's cheat sheet, it is instructed to read params from: Def Map File: 'TEMPLATE_REG-with-POP-AVG_4k_NoFid.deform_map'. If I am using 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730' atlas, which procedure should I follow? Thanks, Mateus Donna Dierker wrote: 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 ___ 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] distance from a node
Hi Donna, That's exactly what I did (although, there are some details in your example that I didn't understand well, see below). But, instead of keep going forth and back selecting nodes and subtracting their coordinates values (I had to do it quite often), I was wondering if there was not an utility that would automatically highlight all the nodes that are at a given distance from my reference point. I am not saying that it is a necessary utility, but, if it was already implemented, I could benefit from it... Thanks, Mateus For example, there's a pretty big x and z offset between this occipital pole (first) and candidate most-posterior calcarine border point: In this example, I though that the biggest offset was for Y (dX: 15-28=-13; dY: -110 --78=32; dZ: -22 --6=-16). That's why you first chose to adjust the Y distance, no? Node 20734 Main Window Inflated XYZ: 15.015987396, -110.156700134, -22.251829147 Shape: -2.904558420 -2.124466896 Node 32819 Main Window Inflated XYZ: 27.664737701, -77.988800049, -6.281192303 Distance: 38.076580048 Shape: -10.455765724 -8.209010124 So I compute -110 - -78 = 32 -- so this point is 32mm from the occipital pole, so we need to find one whose y component of the inflated coordinate is closer to like -110 + 24 = -86. Hope this helps! On 11/30/2006 06:53 AM, Mateus Joffily wrote: Hi David, Thanks for your reply. I asked for this capability because I am trying to perform a spherical registration. Many landmarks are defined as starting and terminating at a certain distance from an anatomical reference point. I thought that a tool, which allows the user to enter a reference point coordinate in the surface and, after, displays every node that is at a given geodesic distance from it, would be helpful This capability is not essential for me. I was wondering if it was already implemented in Caret. Best regards, Mateus David Vanessen wrote: Mateus, First, it is important to clarify whether your request pertains to nodes (as stated) or to foci. In Caret terminology, nodes refers specifically to the points that make up a surface and have locations specified within a coordinate file. Foci refers to stereotaxically identified locations (typically fMRI activation centers) that are specified within a foci file or foci projection file. I'm guessing you are referring to foci, but let us know. At present, I don't think that the capability you are asking about exists for either nodes or foci. If you can let us know what you will be using this for and whether this is a pressing need, it will help us to prioritize the request. Also, if other Caret users would like to see this functionality, let us know. Best regards, David On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote: 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.) ___ 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] distance from a node
I already started having fun with Caret! ;-) Thank you very much Donna Dierker wrote: Come to think of it, I would benefit from that utility, too.;-) Even better would be an accurate, automated border drawing utility. Kidding aside, we recognize this is a highly desirable enhancement, but pretty tough to deliver right now. John Harwell has added some caret_command features that can trim some of the easy ones (e.g., calcarine posterior, central dorsal/medial): SURFACE BORDER EXTREMA caret_command -surface-border-extrema \ input-topo-file input-coord-file input-border-file border-name List the extrema for the surface, the extrema for the border, and the difference between the extrema. -- SURFACE BORDER NIBBLER (remove border points within a distance to surface ext rema) caret_command -surface-border-nibbler \ input-topo-file input-coord-file input-border-file border-name output-border-file surface-extrema-name-or-node-indicator surface-extrema-offset-or-node-number pos-neg Remove points from the named border that are within that are on a . specified side of a surface extrema or node number. But your idea is kind of interesting. Meanwhile, if you choose reference points which differ primarily along the axis of interest, then the distance is a good proxy for the component difference, so no math required. In either case, you'll be surprised how fast you get good at guessing. Before long, you'll need only a few tries, and it's always fun when your first guess is right. ;-) On 11/30/2006 12:52 PM, Mateus Joffily wrote: Hi Donna, That's exactly what I did (although, there are some details in your example that I didn't understand well, see below). But, instead of keep going forth and back selecting nodes and subtracting their coordinates values (I had to do it quite often), I was wondering if there was not an utility that would automatically highlight all the nodes that are at a given distance from my reference point. I am not saying that it is a necessary utility, but, if it was already implemented, I could benefit from it... Thanks, Mateus For example, there's a pretty big x and z offset between this occipital pole (first) and candidate most-posterior calcarine border point: In this example, I though that the biggest offset was for Y (dX: 15-28=-13; dY: -110 --78=32; dZ: -22 --6=-16). That's why you first chose to adjust the Y distance, no? Node 20734 Main Window Inflated XYZ: 15.015987396, -110.156700134, -22.251829147 Shape: -2.904558420 -2.124466896 Node 32819 Main Window Inflated XYZ: 27.664737701, -77.988800049, -6.281192303 Distance: 38.076580048 Shape: -10.455765724 -8.209010124 So I compute -110 - -78 = 32 -- so this point is 32mm from the occipital pole, so we need to find one whose y component of the inflated coordinate is closer to like -110 + 24 = -86. Hope this helps! On 11/30/2006 06:53 AM, Mateus Joffily wrote: Hi David, Thanks for your reply. I asked for this capability because I am trying to perform a spherical registration. Many landmarks are defined as starting and terminating at a certain distance from an anatomical reference point. I thought that a tool, which allows the user to enter a reference point coordinate in the surface and, after, displays every node that is at a given geodesic distance from it, would be helpful This capability is not essential for me. I was wondering if it was already implemented in Caret. Best regards, Mateus David Vanessen wrote: Mateus, First, it is important to clarify whether your request pertains to nodes (as stated) or to foci. In Caret terminology, nodes refers specifically to the points that make up a surface and have locations specified within a coordinate file. Foci refers to stereotaxically identified locations (typically fMRI activation centers) that are specified within a foci file or foci projection file. I'm guessing you are referring to foci, but let us know. At present, I don't think that the capability you are asking about exists for either nodes or foci. If you can let us know what you will be using this for and whether this is a pressing need, it will help us to prioritize the request. Also, if other Caret users would like to see this functionality, let us know. Best regards, David On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote: 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
