[caret-users] using caret for a meta-analysis
Hi, I am in the process of doing a meta-analysis of imaging data. I am a complete novice to Caret, but from a quick look it seems it's stereotaxic foci functions would be ideal to log the peak activity data from different studies. Eventually I would like to display symbols for each peak on a 3D brain rendering of some sort. Perhaps Naively, I thought I could load a template brain (open a spec file), add foci (assuming for a moment I have all coordinates in MNI space) using for example 'layersfocimap stererotaxic focus', and see them pop-out on the brain. However, at first pass, I run into the following questions: a) What brain (spec file) should I load from the fMRI_mapping folder? There are so many of them. Is there anywhere a text file describing what these different files are? b) If I enter a focus with coordinates which happen to be under the surface by a few millimeters, they don't show up on the surface. Is there a way to project them to the surface or to make the brain 'transparent'? c) Once I have the foci entered, can I project them to an inflated brain, and if so, how? Finally, I assume I am not the first to want to use Caret for this purpose - does someone have a 'recipe' for such a project or tips on what pitfalls to avoid? Thanks, Leon Dr. Leon Y Deouell, MD, PhD Department of Psychology The Hebrew University of Jerusalem Jerusalem 91905 Israel Tel: +972-2-5881739 Fax: +972-2-5825659 http://pissaro.soc.huji.ac.il/~leon/Lab
RE: [caret-users] using caret for a meta-analysis
Hi Shawn, Just what I was hoping for. Many thanks. Best, Leon _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Christ, Shawn E. Sent: Friday, December 08, 2006 6:25 PM To: caret-users@brainvis.wustl.edu Subject: RE: [caret-users] using caret for a meta-analysis Hi Leon, I have been working with David, Donna, and John on utilizing Caret for precisely this purpose with respect to an ALE-type meta-analysis on deception that we have submitted for publication. You can download a copy of our spec file, etc. at http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996 I've also uploaded a copy of my personal notes on how to transform foci using Caret. They can be found at http://www.shawnchrist.com/FociTransform.pdf I hope this helps! Best, -Shawn -- Shawn Christ, Ph.D. Assistant Professor Department of Psychological Sciences University of Missouri-Columbia 210 McAlester Hall Columbia, MO 65211 [EMAIL PROTECTED] _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Leon Deouell Sent: Friday, December 08, 2006 9:50 AM To: caret-users@brainvis.wustl.edu Subject: [caret-users] using caret for a meta-analysis Hi, I am in the process of doing a meta-analysis of imaging data. I am a complete novice to Caret, but from a quick look it seems it's stereotaxic foci functions would be ideal to log the peak activity data from different studies. Eventually I would like to display symbols for each peak on a 3D brain rendering of some sort. Perhaps Naively, I thought I could load a template brain (open a spec file), add foci (assuming for a moment I have all coordinates in MNI space) using for example 'layersfocimap stererotaxic focus', and see them pop-out on the brain. However, at first pass, I run into the following questions: a) What brain (spec file) should I load from the fMRI_mapping folder? There are so many of them. Is there anywhere a text file describing what these different files are? b) If I enter a focus with coordinates which happen to be under the surface by a few millimeters, they don't show up on the surface. Is there a way to project them to the surface or to make the brain 'transparent'? c) Once I have the foci entered, can I project them to an inflated brain, and if so, how? Finally, I assume I am not the first to want to use Caret for this purpose - does someone have a 'recipe' for such a project or tips on what pitfalls to avoid? Thanks, Leon Dr. Leon Y Deouell, MD, PhD Department of Psychology The Hebrew University of Jerusalem Jerusalem 91905 Israel Tel: +972-2-5881739 Fax: +972-2-5825659 http://pissaro.soc.huji.ac.il/~leon/Lab
Re: [caret-users] using caret for a meta-analysis
Hi Leon, Shawn has done exactly what you want to do, so if anyone knows the pitfalls, he does. ;-) Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 of this tutorial, if you haven't done so already: CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200 This tutorial includes a spec file intended for this purpose. The ones in the Caret fmri_mapping directory are not really intended for use as visualization specs; rather, Caret uses them when mapping fMRI data onto PALS_B12. You can, however, use the average fiducial surfaces in that directory for your foci-related purposes. Note that studies report results in stereotactic spaces other than MNI (e.g., AFNI users report true Talairach-Tournoux (T88) coordinates, which differs significantly from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; wustl.edu researchers typically use 711-2* space -- somewhere between T88 and MNI). See http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional details. Reading tutorial section 5.2 may clarify some of this, but you're likely to have residual questions/confusion about these spaces. On 12/08/2006 10:24 AM, Christ, Shawn E. wrote: Hi Leon, I have been working with David, Donna, and John on utilizing Caret for precisely this purpose with respect to an ALE-type meta-analysis on deception that we have submitted for publication. You can download a copy of our spec file, etc. at http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996 I’ve also uploaded a copy of my personal notes on how to transform foci using Caret. They can be found at http://www.shawnchrist.com/FociTransform.pdf I hope this helps! Best, -Shawn -- Shawn Christ, Ph.D. Assistant Professor Department of Psychological Sciences University of Missouri-Columbia 210 McAlester Hall Columbia, MO 65211 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *From:* [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] *On Behalf Of *Leon Deouell *Sent:* Friday, December 08, 2006 9:50 AM *To:* caret-users@brainvis.wustl.edu *Subject:* [caret-users] using caret for a meta-analysis Hi, I am in the process of doing a meta-analysis of imaging data. I am a complete novice to Caret, but from a quick look it seems it's stereotaxic foci functions would be ideal to log the peak activity data from different studies. Eventually I would like to display symbols for each peak on a 3D brain rendering of some sort. Perhaps Naively, I thought I could load a template brain (open a spec file), add foci (assuming for a moment I have all coordinates in MNI space) using for example 'layersfocimap stererotaxic focus', and see them pop-out on the brain. However, at first pass, I run into the following questions: a) What brain (spec file) should I load from the fMRI_mapping folder? There are so many of them. Is there anywhere a text file describing what these different files are? b) If I enter a focus with coordinates which happen to be under the surface by a few millimeters, they don't show up on the surface. Is there a way to project them to the surface or to make the brain 'transparent'? c) Once I have the foci entered, can I project them to an inflated brain, and if so, how? Finally, I assume I am not the first to want to use Caret for this purpose – does someone have a 'recipe' for such a project or tips on what pitfalls to avoid? Thanks, Leon Dr. Leon Y Deouell, MD, PhD Department of Psychology The Hebrew University of Jerusalem Jerusalem 91905 Israel Tel: +972-2-5881739 Fax: +972-2-5825659 http://pissaro.soc.huji.ac.il/~leon/Lab http://pissaro.soc.huji.ac.il/%7Eleon/Lab ___ 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] using caret for a meta-analysis
Dear Donna, Thanks for the information. I realize the issue of different coordinate spaces. What I am not sure of is this: If I specify the original space (e.g., T88 or SPM2) for each study in the foci text file, or in the study tab when entering individual foci using the GUI (5.2.2 in the tutorial), will Caret take this into consideration when projecting to the PALS brain? Or do I have to go through some intermediate of transforming from one space to another? Originally I was considering using the tal2mni Matlab function from the Cambridge imagers web site you mentioned to get all coordinates into MNI space, but maybe this is redundant in Caret. Thanks, Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 08, 2006 6:34 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] using caret for a meta-analysis Hi Leon, Shawn has done exactly what you want to do, so if anyone knows the pitfalls, he does. ;-) Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 of this tutorial, if you haven't done so already: CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200 This tutorial includes a spec file intended for this purpose. The ones in the Caret fmri_mapping directory are not really intended for use as visualization specs; rather, Caret uses them when mapping fMRI data onto PALS_B12. You can, however, use the average fiducial surfaces in that directory for your foci-related purposes. Note that studies report results in stereotactic spaces other than MNI (e.g., AFNI users report true Talairach-Tournoux (T88) coordinates, which differs significantly from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; wustl.edu researchers typically use 711-2* space -- somewhere between T88 and MNI). See http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional details. Reading tutorial section 5.2 may clarify some of this, but you're likely to have residual questions/confusion about these spaces. On 12/08/2006 10:24 AM, Christ, Shawn E. wrote: Hi Leon, I have been working with David, Donna, and John on utilizing Caret for precisely this purpose with respect to an ALE-type meta-analysis on deception that we have submitted for publication. You can download a copy of our spec file, etc. at http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996 I've also uploaded a copy of my personal notes on how to transform foci using Caret. They can be found at http://www.shawnchrist.com/FociTransform.pdf I hope this helps! Best, -Shawn -- Shawn Christ, Ph.D. Assistant Professor Department of Psychological Sciences University of Missouri-Columbia 210 McAlester Hall Columbia, MO 65211 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *From:* [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] *On Behalf Of *Leon Deouell *Sent:* Friday, December 08, 2006 9:50 AM *To:* caret-users@brainvis.wustl.edu *Subject:* [caret-users] using caret for a meta-analysis Hi, I am in the process of doing a meta-analysis of imaging data. I am a complete novice to Caret, but from a quick look it seems it's stereotaxic foci functions would be ideal to log the peak activity data from different studies. Eventually I would like to display symbols for each peak on a 3D brain rendering of some sort. Perhaps Naively, I thought I could load a template brain (open a spec file), add foci (assuming for a moment I have all coordinates in MNI space) using for example 'layersfocimap stererotaxic focus', and see them pop-out on the brain. However, at first pass, I run into the following questions: a) What brain (spec file) should I load from the fMRI_mapping folder? There are so many of them. Is there anywhere a text file describing what these different files are? b) If I enter a focus with coordinates which happen to be under the surface by a few millimeters, they don't show up on the surface. Is there a way to project them to the surface or to make the brain 'transparent'? c) Once I have the foci entered, can I project them to an inflated brain, and if so, how? Finally, I assume I am not the first to want to use Caret for this purpose - does someone have a 'recipe' for such a project or tips on what pitfalls to avoid? Thanks, Leon Dr. Leon Y Deouell, MD, PhD Department of Psychology The Hebrew University of Jerusalem Jerusalem 91905 Israel Tel: +972-2-5881739 Fax: +972-2-5825659 http://pissaro.soc.huji.ac.il/~leon/Lab http://pissaro.soc.huji.ac.il/%7Eleon/Lab ___ caret-users mailing list
Re: [caret-users] using caret for a meta-analysis
On 12/08/2006 11:44 AM, Leon Deouell wrote: Dear Donna, Thanks for the information. I realize the issue of different coordinate spaces. What I am not sure of is this: If I specify the original space (e.g., T88 or SPM2) for each study in the foci text file, or in the study tab when entering individual foci using the GUI (5.2.2 in the tutorial), will Caret take this into consideration when projecting to the PALS brain? Yes Or do I have to go through some intermediate of transforming from one space to another? Originally I was considering using the tal2mni Matlab function from the Cambridge imagers web site you mentioned to get all coordinates into MNI space, but maybe this is redundant in Caret. The idea is to make this unnecessary -- as long as the stereotaxic space in question is well-represented by one of these: 711-2C AFNI FLIRT MRITOTAL SPM2 SPM95 SPM96 SPM99 Thanks, Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 08, 2006 6:34 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] using caret for a meta-analysis Hi Leon, Shawn has done exactly what you want to do, so if anyone knows the pitfalls, he does. ;-) Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 of this tutorial, if you haven't done so already: CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200 This tutorial includes a spec file intended for this purpose. The ones in the Caret fmri_mapping directory are not really intended for use as visualization specs; rather, Caret uses them when mapping fMRI data onto PALS_B12. You can, however, use the average fiducial surfaces in that directory for your foci-related purposes. Note that studies report results in stereotactic spaces other than MNI (e.g., AFNI users report true Talairach-Tournoux (T88) coordinates, which differs significantly from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; wustl.edu researchers typically use 711-2* space -- somewhere between T88 and MNI). See http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional details. Reading tutorial section 5.2 may clarify some of this, but you're likely to have residual questions/confusion about these spaces. On 12/08/2006 10:24 AM, Christ, Shawn E. wrote: Hi Leon, I have been working with David, Donna, and John on utilizing Caret for precisely this purpose with respect to an ALE-type meta-analysis on deception that we have submitted for publication. You can download a copy of our spec file, etc. at http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996 I've also uploaded a copy of my personal notes on how to transform foci using Caret. They can be found at http://www.shawnchrist.com/FociTransform.pdf I hope this helps! Best, -Shawn -- Shawn Christ, Ph.D. Assistant Professor Department of Psychological Sciences University of Missouri-Columbia 210 McAlester Hall Columbia, MO 65211 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *From:* [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] *On Behalf Of *Leon Deouell *Sent:* Friday, December 08, 2006 9:50 AM *To:* caret-users@brainvis.wustl.edu *Subject:* [caret-users] using caret for a meta-analysis Hi, I am in the process of doing a meta-analysis of imaging data. I am a complete novice to Caret, but from a quick look it seems it's stereotaxic foci functions would be ideal to log the peak activity data from different studies. Eventually I would like to display symbols for each peak on a 3D brain rendering of some sort. Perhaps Naively, I thought I could load a template brain (open a spec file), add foci (assuming for a moment I have all coordinates in MNI space) using for example 'layersfocimap stererotaxic focus', and see them pop-out on the brain. However, at first pass, I run into the following questions: a) What brain (spec file) should I load from the fMRI_mapping folder? There are so many of them. Is there anywhere a text file describing what these different files are? b) If I enter a focus with coordinates which happen to be under the surface by a few millimeters, they don't show up on the surface. Is there a way to project them to the surface or to make the brain 'transparent'? c) Once I have the foci entered, can I project them to an inflated brain, and if so, how? Finally, I assume I am not the first to want to use Caret for this purpose - does someone have a 'recipe' for such a project or tips on what pitfalls to avoid? Thanks, Leon Dr. Leon Y Deouell, MD, PhD Department of Psychology The Hebrew University of Jerusalem Jerusalem 91905 Israel Tel: +972-2-5881739 Fax: +972-2-5825659 http://pissaro.soc.huji.ac.il/~leon/Lab
