[caret-users] Threshold cluster size
Hello everyone, I'm a new Caret user and am currently trying to display t-contrast fMRI images (SPM99) in Caret. What kind of threshold does Caret require (Display control -- metric -- threshold Pos)? I performed uncorrected t-tests in SPM with p .001. Is 0,001 the value to insert? And how would you let Caret know that a threshold refers to correction for multiple comparisons? If you only want those voxels displayed that exceed a given cluster size (e.g. minimal cluster size = 20 adjacent voxels), how would you go about? Thank you for your help Katja -- Dipl.Psych. Katja Umla-Runge Saarland University Department of Psychologyphone: +49 - (0)681 - 302 4643 P.O.Box 151150 fax: +49 - (0)681 - 302 4049 D-66041 Saarbrueckenemail: [EMAIL PROTECTED] www.BrainCog.de
Re: [caret-users] Latitude/Longitude
Hi Mateus, The copy of the file you included does not have valid latitude longitude values. Latitude should range from -90 to +90 and Longitude should range -180 to +180. The problem is that Caret is not reading binary format latitude longitude files correctly and I have just fixed this problem. In addition, I have modified the Surface Region of Interest Dialog to allow node selection based upon a range of Lat/Long values. Let me know which operating system you are using and I will make an updated version of Caret available for you to download. Lastly, it is probably not a good idea to include caret data files in emails as they can make the messages very large. If needed, we do have a website where files can be uploaded. -- 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 Jun 14, 2007, at 3:45 AM, Mateus Joffily wrote: John, Thank you for the detailed explanation. I followed it, but I am not confident that I got the correct result. To be sure that there was not a problem with my lat/lon file, I decided to test it with CARET_TUTORIAL_SEPT06/PAL_B12.BOTH- HEMS.STANDARD-SCENES.73730.spec. I am attaching the images that I captured from the created metric columns LAT and LONG. The LONG column has only zeros and the LAT column has some strange values. Instead, I would expect a grading of values along the latitude- longitude isocontours. Is it correct? I am also attaching a copy of the latlon file (PALS_B12.LR.73730.latlon) converted to metric. Thanks, Mateus John Harwell wrote: Mateus, We will add ROI node selection with latitude/longitude to our to- do list. First, convert the LatLon file to a Metric file: * Write your latitude/longitude file and be sure that Data File Encoding at the bottom of the Save Data File Dialog is set to Ascii (Text). * Load the lat/lon file into a text editor. * Change tag-version 1 to tag-version 2 * Change tag-number-of-columns 1 to tag-number-of-columns 4 * Save the lat/lon file * Change then name of the lat-lon file so that it ends with .metric. * Select File Menu-Open Data File. Set the type to Metric, choose the file, and press the Open button. A Dialog will appear listing the columns for loading. Set the names of the first two columns to Long and Lat respectively. Second, to select the ROI * Use the Display Control to set the displayed metric to Lat. * On the Surface ROI Dialog, set the selection method to Nodes with Metric. * Set the Thresholds to the range of latitudes you want to select. * Press the Select Nodes button. * On the Display Control Dialog, change the selected metric to Long. * On the Surface ROI Dialog, change Normal Selection to And Selection (Intersection). * Set the thresholds to the range of longitudes you want to select. * Press the Select Nodes button. -- 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 Jun 13, 2007, at 11:13 AM, Mateus Joffily wrote: Hi, I would like to select every node that is inside a certain range of latitude/longitude coordinates. I thought to create a metric column with the nodes' longitude and latitude values and then use the 'Node with Metric' operation from 'Surface Region of Interest' dialog to select the nodes. But I am not sure it is the easiest way of doing it... Does anyone has any suggestion? Thank you very much. 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
Re: [caret-users] Threshold cluster size
Hi Katja, The thresholds only display values greater than the threshold value. So you could use the metric math dialog (Attributes Menu-Metric- Mathematical Operations to convert your p-values to (1 - p) values (I may have seen this called Q) and then set the threshold to 0.999. On the Metric Math Dialog, set both Column A and Result to your metric data. Check the button next to Multiply Column A by Scalar, enter -1.0 for the value, and press the Apply button. Next, check the button next to Add Scalar to Column A, enter 1.0 for the value, and press the Apply button. To find clusters use Attributes Menu-Metric-Clustering and Smoothing. Press the Help button and it will describe how to use the clustering option. You can also use the threshold values for the clusters to find only nodes with values less than 0.001. -- 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 Jun 15, 2007, at 9:04 AM, Katja Umla-Runge wrote: Hello everyone, I'm a new Caret user and am currently trying to display t-contrast fMRI images (SPM99) in Caret. What kind of threshold does Caret require (Display control -- metric -- threshold Pos)? I performed uncorrected t-tests in SPM with p .001. Is 0,001 the value to insert? And how would you let Caret know that a threshold refers to correction for multiple comparisons? If you only want those voxels displayed that exceed a given cluster size (e.g. minimal cluster size = 20 adjacent voxels), how would you go about? Thank you for your help Katja -- Dipl.Psych. Katja Umla-Runge Saarland University Department of Psychologyphone: +49 - (0)681 - 302 4643 P.O.Box 151150 fax: +49 - (0)681 - 302 4049 D-66041 Saarbrueckenemail: [EMAIL PROTECTED] www.BrainCog.de ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Latitude/Longitude
Hi John, Thank you very much. Sorry for the large attachment. I just realized the message size, after sending it. My operating system is Linux. Thanks again, Mateus John Harwell wrote: Hi Mateus, The copy of the file you included does not have valid latitude longitude values. Latitude should range from -90 to +90 and Longitude should range -180 to +180. The problem is that Caret is not reading binary format latitude longitude files correctly and I have just fixed this problem. In addition, I have modified the Surface Region of Interest Dialog to allow node selection based upon a range of Lat/Long values. Let me know which operating system you are using and I will make an updated version of Caret available for you to download. Lastly, it is probably not a good idea to include caret data files in emails as they can make the messages very large. If needed, we do have a website where files can be uploaded. -- 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 Jun 14, 2007, at 3:45 AM, Mateus Joffily wrote: John, Thank you for the detailed explanation. I followed it, but I am not confident that I got the correct result. To be sure that there was not a problem with my lat/lon file, I decided to test it with CARET_TUTORIAL_SEPT06/PAL_B12.BOTH- HEMS.STANDARD-SCENES.73730.spec. I am attaching the images that I captured from the created metric columns LAT and LONG. The LONG column has only zeros and the LAT column has some strange values. Instead, I would expect a grading of values along the latitude- longitude isocontours. Is it correct? I am also attaching a copy of the latlon file (PALS_B12.LR.73730.latlon) converted to metric. Thanks, Mateus John Harwell wrote: Mateus, We will add ROI node selection with latitude/longitude to our to- do list. First, convert the LatLon file to a Metric file: * Write your latitude/longitude file and be sure that Data File Encoding at the bottom of the Save Data File Dialog is set to Ascii (Text). * Load the lat/lon file into a text editor. * Change tag-version 1 to tag-version 2 * Change tag-number-of-columns 1 to tag-number-of-columns 4 * Save the lat/lon file * Change then name of the lat-lon file so that it ends with .metric. * Select File Menu-Open Data File. Set the type to Metric, choose the file, and press the Open button. A Dialog will appear listing the columns for loading. Set the names of the first two columns to Long and Lat respectively. Second, to select the ROI * Use the Display Control to set the displayed metric to Lat. * On the Surface ROI Dialog, set the selection method to Nodes with Metric. * Set the Thresholds to the range of latitudes you want to select. * Press the Select Nodes button. * On the Display Control Dialog, change the selected metric to Long. * On the Surface ROI Dialog, change Normal Selection to And Selection (Intersection). * Set the thresholds to the range of longitudes you want to select. * Press the Select Nodes button. -- 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 Jun 13, 2007, at 11:13 AM, Mateus Joffily wrote: Hi, I would like to select every node that is inside a certain range of latitude/longitude coordinates. I thought to create a metric column with the nodes' longitude and latitude values and then use the 'Node with Metric' operation from 'Surface Region of Interest' dialog to select the nodes. But I am not sure it is the easiest way of doing it... Does anyone has any suggestion? Thank you very much. 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] Latitude/Longitude
Mateus, Go to the website http://brainmap.wustl.edu/pub/john/;. You will need to use the username pub and the password download. Get the file caret5_exe_linux.zip which contains only the caret5 executable. Place it into your caret installation's bin directory. Be sure to back up your existing bin/caret5 in case you run into problems with this new caret5. -- 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 Jun 15, 2007, at 10:53 AM, Mateus Joffily wrote: Hi John, Thank you very much. Sorry for the large attachment. I just realized the message size, after sending it. My operating system is Linux. Thanks again, Mateus John Harwell wrote: Hi Mateus, The copy of the file you included does not have valid latitude longitude values. Latitude should range from -90 to +90 and Longitude should range -180 to +180. The problem is that Caret is not reading binary format latitude longitude files correctly and I have just fixed this problem. In addition, I have modified the Surface Region of Interest Dialog to allow node selection based upon a range of Lat/Long values. Let me know which operating system you are using and I will make an updated version of Caret available for you to download. Lastly, it is probably not a good idea to include caret data files in emails as they can make the messages very large. If needed, we do have a website where files can be uploaded. -- 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 Jun 14, 2007, at 3:45 AM, Mateus Joffily wrote: John, Thank you for the detailed explanation. I followed it, but I am not confident that I got the correct result. To be sure that there was not a problem with my lat/lon file, I decided to test it with CARET_TUTORIAL_SEPT06/ PAL_B12.BOTH- HEMS.STANDARD-SCENES.73730.spec. I am attaching the images that I captured from the created metric columns LAT and LONG. The LONG column has only zeros and the LAT column has some strange values. Instead, I would expect a grading of values along the latitude- longitude isocontours. Is it correct? I am also attaching a copy of the latlon file (PALS_B12.LR. 73730.latlon) converted to metric. Thanks, Mateus John Harwell wrote: Mateus, We will add ROI node selection with latitude/longitude to our to- do list. First, convert the LatLon file to a Metric file: * Write your latitude/longitude file and be sure that Data File Encoding at the bottom of the Save Data File Dialog is set to Ascii (Text). * Load the lat/lon file into a text editor. * Change tag-version 1 to tag-version 2 * Change tag-number-of-columns 1 to tag-number-of-columns 4 * Save the lat/lon file * Change then name of the lat-lon file so that it ends with .metric. * Select File Menu-Open Data File. Set the type to Metric, choose the file, and press the Open button. A Dialog will appear listing the columns for loading. Set the names of the first two columns to Long and Lat respectively. Second, to select the ROI * Use the Display Control to set the displayed metric to Lat. * On the Surface ROI Dialog, set the selection method to Nodes with Metric. * Set the Thresholds to the range of latitudes you want to select. * Press the Select Nodes button. * On the Display Control Dialog, change the selected metric to Long. * On the Surface ROI Dialog, change Normal Selection to And Selection (Intersection). * Set the thresholds to the range of longitudes you want to select. * Press the Select Nodes button. -- 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 Jun 13, 2007, at 11:13 AM, Mateus Joffily wrote: Hi, I would like to select every node that is inside a certain range of latitude/longitude coordinates. I thought to create a metric column with the nodes' longitude and latitude values and then use the 'Node with Metric' operation from 'Surface Region of Interest' dialog to select the nodes. But I am not sure it is the easiest way of doing it... Does anyone has any suggestion? Thank you very much. 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
