Re: [caret-users] MNI coordinate - additional information on stereotaxic foci
Dear caret experts, Even after getting my head around the suggested documents ,I have not found the good response for how to obtain the MNI coordinate of mapped activation on flat brain.If one click on the activation which is shown in the main window,the identity window will pop up but the XYZ coordinate of the voxel is not in MNI space,is it? I will really appreciate if someone gives me a good clue of how obtaining the MNI coordinate of our activation ? Is it possible to provide [X,Y,Z ] in MNI coordinate and then ask Caret to show this coordinate on the flat brain? Thanks, Alireza --- On Mon, 10/27/08, David Van Essen [EMAIL PROTECTED] wrote: From: David Van Essen [EMAIL PROTECTED] Subject: Re: [caret-users] MNI coordinate - additional information on stereotaxic foci To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Cc: [EMAIL PROTECTED] Date: Monday, October 27, 2008, 9:42 PM Alireza, To expand on what Donna said, The foci and foci projection (fociproj) file types in Caret are likely to be useful for the needs that you describe. For example, if you enter the center of your ROI as a stereotaxic focus in an identified stereotaxic space, you can then project it to the PALS atlas surface and view it in any of the various other stereotaxic spaces that PALS has been mapped to. You can also view it in volume slices as well as on the atlas flat maps. You can in addition compare your coordinate data, to the collection of 31,000 stereotaxic foci from 1,000 published studies that we have recently added to our SumsDB database and made freely available. The tutorial document and dataset that Donna referred to (http://sumsdb.wustl.edu/sums/directory.do?id=6617378; STEREOTAXIC_FOCI_TUTORIAL/ directory) show how to download, search, and view the existing foci. However, it is still in 'beta-test' mode. I just now replaced the previous pdf document and associated dataset with newer versions that correct various minor errors. If you started taking a look at the previous version, please switch to the newer one, and also let us know if there are persisting glitches or matters needing clarification. We are nearing completion of a separate tutorial document that describes how to generate foci files and import them into a 'Foci Library' that will be introduced into SumsDB. Stay tuned for an announcement regarding that. David VE On Oct 25, 2008, at 8:41 AM, Donna Dierker wrote: Hi Alireza, Sorry for the delayed reply, but you happened to catch us at a workshop on human consciousness; I normally don't work on Saturday, but I'm headed to day 2 shortly. A full reply would take more time than I have, but the short answer is that I don't think Caret does quite what you want -- yet. I think there is a spatial query under development in sumsdb, but it isn't quite ready for prime time yet. That said, you might check out the foci tutorial here: STEREOTAXIC_FOCI http://sumsdb.wustl.edu/sums/directory.do?id=6617378 Just scan the PDF; you'll be able to tell if it's useful. Another source to try is here: http://brainmap.org/ While this isn't flat map related, you might still find it useful. One could write a script/program that would find the closest node on the SPM*/FLIRT/MRITOTAL PALS surface to any given MNI coordinate, and then lookup the paint attributes associated with that node, but I don't know of an existing utility that makes it easy. Donna On 10/24/2008 08:35 AM, Alireza Salamy wrote: Dear Caret experts, I have mapped my functional data from SPM5 on flat brain using latest version of Caret and now I would like to check some specific activation(I expected to be among the activations which has been mapped on flat brain) like [x,y,Z](MNI coordinate).one bothering way would be click on each activation and see if the coordinate that comes up in voxel(anatomy) section is the same.but first of all do the [X,Y,Z] coordinate which is reported by voxel anatomy shows MNI coordinate?second,is there a better way of entering MNI coordinate and see the corresponding region to that? lets say entering[x,y,z] (MNI coordinate)and see where is that coordinate on the flat brain? Thanks, Alireza ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] MNI coordinate - additional information on stereotaxic foci
Hi Alireza, I hope the inline reply below is more clear. Donna On 11/03/2008 10:59 AM, Alireza Salamy wrote: Dear caret experts, Even after getting my head around the suggested documents ,I have not found the good response for how to obtain the MNI coordinate of mapped activation on flat brain.If one click on the activation which is shown in the main window,the identity window will pop up but the XYZ coordinate of the voxel is not in MNI space,is it? Before clicking on the flat map, use File: Open Data File: file type coordinate file. If your current directory doesn't have one of these files in it, then navigate to the /your_caret_path/caret/data_files/fmri_mapping_files directory and load one of these files: Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_MRITOTAL.clean.73730.coord Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM99.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_MRITOTAL.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM99.clean.73730.coord Ideally, the file should match whatever was used to map the data. After you load this file, you can switch back to the flat map view in the main window, but select Window: Window 2 and select the fiducial coordinate file just loaded in Window 2. Now click on your flat map activation: The fiducial coordinate will print in the ID window. Likewise, if you have several clusters of activation for which you want the COG, see the previous post about generating a cluster report on a metric file. Make sure you use the appropriate MNI fiducial coordinate file when you select the nodes in the Surface: Region of interest dialog, because the COG will be relative to this fiducial coord file. I will really appreciate if someone gives me a good clue of how obtaining the MNI coordinate of our activation ? Is it possible to provide [X,Y,Z ] in MNI coordinate and then ask Caret to show this coordinate on the flat brain? Thanks, Alireza --- On *Mon, 10/27/08, David Van Essen /[EMAIL PROTECTED]/* wrote: From: David Van Essen [EMAIL PROTECTED] Subject: Re: [caret-users] MNI coordinate - additional information on stereotaxic foci To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Cc: [EMAIL PROTECTED] Date: Monday, October 27, 2008, 9:42 PM Alireza, To expand on what Donna said, The foci and foci projection (fociproj) file types in Caret are likely to be useful for the needs that you describe. For example, if you enter the center of your ROI as a stereotaxic focus in an identified stereotaxic space, you can then project it to the PALS atlas surface and view it in any of the various other stereotaxic spaces that PALS has been mapped to. You can also view it in volume slices as well as on the atlas flat maps. You can in addition compare your coordinate data, to the collection of 31,000 stereotaxic foci from 1,000 published studies that we have recently added to our SumsDB database and made freely available. The tutorial document and dataset that Donna referred to (http://sumsdb.wustl.edu/sums/directory.do?id=6617378; STEREOTAXIC_FOCI_TUTORIAL/ directory) show how to download, search, and view the existing foci. However, it is still in 'beta-test' mode. I just now replaced the previous pdf document and associated dataset with newer versions that correct various minor errors. If you started taking a look at the previous version, please switch to the newer one, and also let us know if there are persisting glitches or matters needing clarification. We are nearing completion of a separate tutorial document that describes how to generate foci files and import them into a 'Foci Library' that will be introduced into SumsDB. Stay tuned for an announcement regarding that. David VE On Oct 25, 2008, at 8:41 AM, Donna Dierker wrote: Hi Alireza, Sorry for the delayed reply, but you happened to catch us at a workshop on human consciousness; I normally don't work on Saturday, but I'm headed to day 2 shortly. A full reply would take more time than I have, but the short answer is that I don't think Caret does quite what you want -- yet. I think there is a spatial query under development in sumsdb, but it isn't quite ready for prime time yet. That said, you might check out the foci tutorial here: STEREOTAXIC_FOCI http://sumsdb.wustl.edu/sums/directory.do?id=6617378 Just scan the PDF; you'll be able to tell if it's useful. Another source to try is here
Re: [caret-users] MNI coordinate - additional information on stereotaxic foci
Alireza, To expand on what Donna said, The foci and foci projection (fociproj) file types in Caret are likely to be useful for the needs that you describe. For example, if you enter the center of your ROI as a stereotaxic focus in an identified stereotaxic space, you can then project it to the PALS atlas surface and view it in any of the various other stereotaxic spaces that PALS has been mapped to. You can also view it in volume slices as well as on the atlas flat maps. You can in addition compare your coordinate data, to the collection of 31,000 stereotaxic foci from 1,000 published studies that we have recently added to our SumsDB database and made freely available. The tutorial document and dataset that Donna referred to (http://sumsdb.wustl.edu/sums/directory.do?id=6617378 ; STEREOTAXIC_FOCI_TUTORIAL/ directory) show how to download, search, and view the existing foci. However, it is still in 'beta-test' mode. I just now replaced the previous pdf document and associated dataset with newer versions that correct various minor errors. If you started taking a look at the previous version, please switch to the newer one, and also let us know if there are persisting glitches or matters needing clarification. We are nearing completion of a separate tutorial document that describes how to generate foci files and import them into a 'Foci Library' that will be introduced into SumsDB. Stay tuned for an announcement regarding that. David VE On Oct 25, 2008, at 8:41 AM, Donna Dierker wrote: Hi Alireza, Sorry for the delayed reply, but you happened to catch us at a workshop on human consciousness; I normally don't work on Saturday, but I'm headed to day 2 shortly. A full reply would take more time than I have, but the short answer is that I don't think Caret does quite what you want -- yet. I think there is a spatial query under development in sumsdb, but it isn't quite ready for prime time yet. That said, you might check out the foci tutorial here: STEREOTAXIC_FOCI http://sumsdb.wustl.edu/sums/directory.do?id=6617378 Just scan the PDF; you'll be able to tell if it's useful. Another source to try is here: http://brainmap.org/ While this isn't flat map related, you might still find it useful. One could write a script/program that would find the closest node on the SPM*/FLIRT/MRITOTAL PALS surface to any given MNI coordinate, and then lookup the paint attributes associated with that node, but I don't know of an existing utility that makes it easy. Donna On 10/24/2008 08:35 AM, Alireza Salamy wrote: Dear Caret experts, I have mapped my functional data from SPM5 on flat brain using latest version of Caret and now I would like to check some specific activation(I expected to be among the activations which has been mapped on flat brain) like [x,y,Z](MNI coordinate).one bothering way would be click on each activation and see if the coordinate that comes up in voxel(anatomy) section is the same.but first of all do the [X,Y,Z] coordinate which is reported by voxel anatomy shows MNI coordinate?second,is there a better way of entering MNI coordinate and see the corresponding region to that? lets say entering[x,y,z] (MNI coordinate)and see where is that coordinate on the flat brain? Thanks, Alireza ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
