RE: [caret-users] using caret for a meta-analysis
That seems to do the trick. Thanks. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David Vanessen Sent: Sunday, January 07, 2007 7:30 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] using caret for a meta-analysis Leon, I can replicate and explain your observations in the following way: 1) Load a foci file that contains data in multiple stereotaxic spaces, and view the foci with the FLIRT average fiducial surface in the main window.. At this stage, each focus will be in its original space, even though you are viewing the FLIRT average fiducial surface. 2) Open a second Caret window that contains a non-fiducial surface (e.g., the inflated surface). Note that no foci are visible on the inflated surface prior to projection. 3) Apply Layers: Foci: Project Foci to PALS atlas. As the projection process occurs, each focus that didn't start out as already being in FLIRT space will jump to a new position, by an amount that reflects the difference between FLIRT and whatever space the focus originated in. Concurrently, foci will start appearing on the inflated surface. Once the projection process is completed, each focus should be visible only once on the fiducial surface. 4) Open the original foci file (using Open File or using Toolbar: Spec) and Append it to the current foci. Now you should see most (but perhaps not all) foci doubled in the average fiducial surface view but not in the inflated view. In other words, I infer that you inadvertently loaded both the foci and the foci projection file to create the view in your email. In general, you will want to avoid such quasi-duplication. Instead, only view foci projection data once the projection is complete, unless you have a specific need to see the foci in their original space. I hope this resolves your question. David On Jan 7, 2007, at 3:37 AM, Leon Deouell wrote: > Hi, > > I am displaying my foci now(post projection to PALS-B12) on the > FIDUCIAL > Human.PALS_B12.LEFT_AVG_B1-12.FIDICUAL_FLIRT.clean.73730.coord. For > some > reason, it looks like every blob is doubled (see window capture > attached). > I don't see this if I display the same foci on the inflated or > hyperinflated > brains. Any idea why this is happening? > > Thanks, > > Leon > > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Donna > Dierker > Sent: Friday, December 22, 2006 5:17 PM > To: Caret, SureFit, and SuMS software users > Subject: Re: [caret-users] using caret for a meta-analysis > > Thank YOU for figuring out your own problem -- a pretty obscure > one, at > that. > > I agree both minus and long dash should read as minus; I hope it's not > tough for John to do. Sometimes the I/O stuff is QT's domain and > not so > easy to control. > > On 12/22/2006 09:05 AM, Leon Deouell wrote: >> Dear Donna, >> >> Thanks to your critical eye, I found out what the problem is. You >> noted > that >> for focus 4 the description is L Superior Frontal Gyrus but the x > coordinate >> was 20 in your readout. However, in the foci file I've sent, the line >> actually says: >> 4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal >> gyrusPure,,pitch >> >> I am not sure what you used to read the foci file, but it seems this >> software, like CARET, ignored the minus sign, and it turns out >> that all > the >> numbers which were zeroed in CARET, where actually negative >> numbers in my >> original foci file. I tracked the problem back to the character >> used for > the >> minus sign. When I created the excel file (from which I created >> the CSV > foci >> file), I have sometimes cut and paste from PDF files or HTML files >> of the >> original articles. In some cases, the minus sign was a longer dash >> sign >> rather than a real minus sign. They look very similar but the wrong >> character is a slightly longer line if you look at it carefully. >> If you > open >> the foci file I've sent before with Notepad (that is, if you use >> Windows) >> you will see what I mean. When I replaced these characters with >> real minus >> signs, the apparent bug was solved. >> >> I think this is a point to keep in mind because I am pretty sure many > would >> cut and paste when creating large meta-analysis files (I have more >> than > 100 >> points in the full file) rather than retype (which is also more >> prone to >> errors). Maybe CARET can be configured to detect this somehow and >> either >> report the problem or ac
Re: [caret-users] using caret for a meta-analysis
Hi Leon, Is it possible you have both a foci and fociproj file, both of which are loaded? On 01/07/2007 03:37 AM, Leon Deouell wrote: Hi, I am displaying my foci now(post projection to PALS-B12) on the FIDUCIAL Human.PALS_B12.LEFT_AVG_B1-12.FIDICUAL_FLIRT.clean.73730.coord. For some reason, it looks like every blob is doubled (see window capture attached). I don't see this if I display the same foci on the inflated or hyperinflated brains. Any idea why this is happening? Thanks, Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 22, 2006 5:17 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] using caret for a meta-analysis Thank YOU for figuring out your own problem -- a pretty obscure one, at that. I agree both minus and long dash should read as minus; I hope it's not tough for John to do. Sometimes the I/O stuff is QT's domain and not so easy to control. On 12/22/2006 09:05 AM, Leon Deouell wrote: Dear Donna, Thanks to your critical eye, I found out what the problem is. You noted that for focus 4 the description is L Superior Frontal Gyrus but the x coordinate was 20 in your readout. However, in the foci file I've sent, the line actually says: 4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch I am not sure what you used to read the foci file, but it seems this software, like CARET, ignored the minus sign, and it turns out that all the numbers which were zeroed in CARET, where actually negative numbers in my original foci file. I tracked the problem back to the character used for the minus sign. When I created the excel file (from which I created the CSV foci file), I have sometimes cut and paste from PDF files or HTML files of the original articles. In some cases, the minus sign was a longer dash sign rather than a real minus sign. They look very similar but the wrong character is a slightly longer line if you look at it carefully. If you open the foci file I've sent before with Notepad (that is, if you use Windows) you will see what I mean. When I replaced these characters with real minus signs, the apparent bug was solved. I think this is a point to keep in mind because I am pretty sure many would cut and paste when creating large meta-analysis files (I have more than 100 points in the full file) rather than retype (which is also more prone to errors). Maybe CARET can be configured to detect this somehow and either report the problem or accept this other dash sign as minus. Many thanks for the quick response. Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 22, 2006 4:19 PM To: Leon Deouell Cc: 'Caret, SureFit,and SuMS software users' Subject: Re: [caret-users] using caret for a meta-analysis Hi Leon, This looks like a bug to me. I was able to replicate this behavior on my Caret 5.502 12/15/2006 Caret running RHEL. The ID readout for these foci were just fine (readout followed by corresponding line from foci file): Focus 2: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0) 2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch Focus 3: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0) 3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch But these foci had their x or y coordinate component zeroed out: Focus 4: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0) 4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch [Note from Donna: If left SFG, then wouldn't it be -20?) Focus 5: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0) 5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch Focus 6: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0) 6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch On 12/22/2006 03:26 AM, Leon Deouell wrote: Hi, I am finding something peculiar when looking at foci. To illustrate, I created a smaller file with only one study (foci file attached). I went through the following steps: 1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder 2. Opened the foci file test1study.foci 3. Projected the foci using Layers/Foci/Project Foci to PALS atlas (selecting 'project above surface [0.00]). The projected foci can be viewed in the attached figure coordinates.jpg Now I click on foci, and look the Identify Window. I find that for some, the values in 'Original
Re: [caret-users] using caret for a meta-analysis
Leon, I can replicate and explain your observations in the following way: 1) Load a foci file that contains data in multiple stereotaxic spaces, and view the foci with the FLIRT average fiducial surface in the main window.. At this stage, each focus will be in its original space, even though you are viewing the FLIRT average fiducial surface. 2) Open a second Caret window that contains a non-fiducial surface (e.g., the inflated surface). Note that no foci are visible on the inflated surface prior to projection. 3) Apply Layers: Foci: Project Foci to PALS atlas. As the projection process occurs, each focus that didn't start out as already being in FLIRT space will jump to a new position, by an amount that reflects the difference between FLIRT and whatever space the focus originated in. Concurrently, foci will start appearing on the inflated surface. Once the projection process is completed, each focus should be visible only once on the fiducial surface. 4) Open the original foci file (using Open File or using Toolbar: Spec) and Append it to the current foci. Now you should see most (but perhaps not all) foci doubled in the average fiducial surface view but not in the inflated view. In other words, I infer that you inadvertently loaded both the foci and the foci projection file to create the view in your email. In general, you will want to avoid such quasi-duplication. Instead, only view foci projection data once the projection is complete, unless you have a specific need to see the foci in their original space. I hope this resolves your question. David On Jan 7, 2007, at 3:37 AM, Leon Deouell wrote: Hi, I am displaying my foci now(post projection to PALS-B12) on the FIDUCIAL Human.PALS_B12.LEFT_AVG_B1-12.FIDICUAL_FLIRT.clean.73730.coord. For some reason, it looks like every blob is doubled (see window capture attached). I don't see this if I display the same foci on the inflated or hyperinflated brains. Any idea why this is happening? Thanks, Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 22, 2006 5:17 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] using caret for a meta-analysis Thank YOU for figuring out your own problem -- a pretty obscure one, at that. I agree both minus and long dash should read as minus; I hope it's not tough for John to do. Sometimes the I/O stuff is QT's domain and not so easy to control. On 12/22/2006 09:05 AM, Leon Deouell wrote: Dear Donna, Thanks to your critical eye, I found out what the problem is. You noted that for focus 4 the description is L Superior Frontal Gyrus but the x coordinate was 20 in your readout. However, in the foci file I've sent, the line actually says: 4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch I am not sure what you used to read the foci file, but it seems this software, like CARET, ignored the minus sign, and it turns out that all the numbers which were zeroed in CARET, where actually negative numbers in my original foci file. I tracked the problem back to the character used for the minus sign. When I created the excel file (from which I created the CSV foci file), I have sometimes cut and paste from PDF files or HTML files of the original articles. In some cases, the minus sign was a longer dash sign rather than a real minus sign. They look very similar but the wrong character is a slightly longer line if you look at it carefully. If you open the foci file I've sent before with Notepad (that is, if you use Windows) you will see what I mean. When I replaced these characters with real minus signs, the apparent bug was solved. I think this is a point to keep in mind because I am pretty sure many would cut and paste when creating large meta-analysis files (I have more than 100 points in the full file) rather than retype (which is also more prone to errors). Maybe CARET can be configured to detect this somehow and either report the problem or accept this other dash sign as minus. Many thanks for the quick response. Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 22, 2006 4:19 PM To: Leon Deouell Cc: 'Caret, SureFit,and SuMS software users' Subject: Re: [caret-users] using caret for a meta-analysis Hi Leon, This looks like a bug to me. I was able to replicate this behavior on my Caret 5.502 12/15/2006 Caret running RHEL. The ID readout for these foci were just fine (readout followed by corresponding line from foci file): Focus 2: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0) 2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch Focus 3: MolholmEtAl05.pitch Class: pitch Ori
RE: [caret-users] using caret for a meta-analysis
Hi, I am displaying my foci now(post projection to PALS-B12) on the FIDUCIAL Human.PALS_B12.LEFT_AVG_B1-12.FIDICUAL_FLIRT.clean.73730.coord. For some reason, it looks like every blob is doubled (see window capture attached). I don't see this if I display the same foci on the inflated or hyperinflated brains. Any idea why this is happening? Thanks, Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 22, 2006 5:17 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] using caret for a meta-analysis Thank YOU for figuring out your own problem -- a pretty obscure one, at that. I agree both minus and long dash should read as minus; I hope it's not tough for John to do. Sometimes the I/O stuff is QT's domain and not so easy to control. On 12/22/2006 09:05 AM, Leon Deouell wrote: > Dear Donna, > > Thanks to your critical eye, I found out what the problem is. You noted that > for focus 4 the description is L Superior Frontal Gyrus but the x coordinate > was 20 in your readout. However, in the foci file I've sent, the line > actually says: > 4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch > > I am not sure what you used to read the foci file, but it seems this > software, like CARET, ignored the minus sign, and it turns out that all the > numbers which were zeroed in CARET, where actually negative numbers in my > original foci file. I tracked the problem back to the character used for the > minus sign. When I created the excel file (from which I created the CSV foci > file), I have sometimes cut and paste from PDF files or HTML files of the > original articles. In some cases, the minus sign was a longer dash sign > rather than a real minus sign. They look very similar but the wrong > character is a slightly longer line if you look at it carefully. If you open > the foci file I've sent before with Notepad (that is, if you use Windows) > you will see what I mean. When I replaced these characters with real minus > signs, the apparent bug was solved. > > I think this is a point to keep in mind because I am pretty sure many would > cut and paste when creating large meta-analysis files (I have more than 100 > points in the full file) rather than retype (which is also more prone to > errors). Maybe CARET can be configured to detect this somehow and either > report the problem or accept this other dash sign as minus. > > Many thanks for the quick response. > > Leon > > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker > Sent: Friday, December 22, 2006 4:19 PM > To: Leon Deouell > Cc: 'Caret, SureFit,and SuMS software users' > Subject: Re: [caret-users] using caret for a meta-analysis > > Hi Leon, > > This looks like a bug to me. I was able to replicate this behavior on > my Caret 5.502 12/15/2006 Caret running RHEL. The ID readout for these > foci were just fine (readout followed by corresponding line from foci file): > > Focus 2: MolholmEtAl05.pitch Class: pitch > Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0) > 2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch > > Focus 3: MolholmEtAl05.pitch Class: pitch > Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0) > 3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch > > But these foci had their x or y coordinate component zeroed out: > > Focus 4: MolholmEtAl05.pitch Class: pitch > Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0) > 4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch > [Note from Donna: If left SFG, then wouldn't it be -20?) > > Focus 5: MolholmEtAl05.pitch Class: pitch > Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0) > 5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch > > Focus 6: MolholmEtAl05.pitch Class: pitch > Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0) > 6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch > > On 12/22/2006 03:26 AM, Leon Deouell wrote: > >> Hi, >> >> I am finding something peculiar when looking at foci. To illustrate, I >> created a smaller file with only one study (foci file attached). I went >> through the following steps: >> >> 1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the >> /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder >> 2. Opened the foci file test1study.foci >> 3. Projected the foci using Layers/Foci/Project Foci to PALS atlas >> (selecting 'project above surface [0.00]). >> >> The pro
Re: [caret-users] using caret for a meta-analysis
Hello, I have modified Caret to look for these unicode dashes (em-dash, en- dash, etc) that range from 8208 to 8213 when reading a comma separated file. In addition, Caret will now print a message if an invalid character is found in text representations of floating point numbers. John Harwell On Dec 22, 2006, at 9:16 AM, Leon Deouell wrote: Ps. In case this helps any: This is the wrong characther: '-', and this is the right one: '-' . Using abs('-') in Matlab, the wrong one translates to 8211, while the correct minus sign translates to 45. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 22, 2006 4:19 PM To: Leon Deouell Cc: 'Caret, SureFit,and SuMS software users' Subject: Re: [caret-users] using caret for a meta-analysis Hi Leon, This looks like a bug to me. I was able to replicate this behavior on my Caret 5.502 12/15/2006 Caret running RHEL. The ID readout for these foci were just fine (readout followed by corresponding line from foci file): Focus 2: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0) 2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch Focus 3: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0) 3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch But these foci had their x or y coordinate component zeroed out: Focus 4: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0) 4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch [Note from Donna: If left SFG, then wouldn't it be -20?) Focus 5: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0) 5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch Focus 6: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0) 6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch On 12/22/2006 03:26 AM, Leon Deouell wrote: Hi, I am finding something peculiar when looking at foci. To illustrate, I created a smaller file with only one study (foci file attached). I went through the following steps: 1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder 2. Opened the foci file test1study.foci 3. Projected the foci using Layers/Foci/Project Foci to PALS atlas (selecting 'project above surface [0.00]). The projected foci can be viewed in the attached figure coordinates.jpg Now I click on foci, and look the Identify Window. I find that for some, the values in 'Original Sterotaxic Positions' match the coordinates in the foci file. But for some (e.g., the one marked with a red ellipse in the figure) I get one of the coordinates set to zero. For example for this focus, I get: _ Focus 6: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): 41.0 0.0 6.0 Stereotaxic Position (FLIRT): 41.0 0.9 2.1 _ But focus 6 coordinates as specified in the foci file are actually [41, -75, 6] The same happens to a few others (but not all) foci. Sometimes it is the y coordinate that becomes zero, and sometimes the x coordinate. I verified that it is not something to do with the foci projection - the same results are obtained if I click the foci before projection. Any idea what I may be doing wrong, or not interpreting correctly? Thanks, Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 08, 2006 7:49 PM To: Caret, SureFit, and SuMS software users Subject: 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 PROTE
Re: [caret-users] using caret for a meta-analysis
Thank YOU for figuring out your own problem -- a pretty obscure one, at that. I agree both minus and long dash should read as minus; I hope it's not tough for John to do. Sometimes the I/O stuff is QT's domain and not so easy to control. On 12/22/2006 09:05 AM, Leon Deouell wrote: Dear Donna, Thanks to your critical eye, I found out what the problem is. You noted that for focus 4 the description is L Superior Frontal Gyrus but the x coordinate was 20 in your readout. However, in the foci file I've sent, the line actually says: 4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch I am not sure what you used to read the foci file, but it seems this software, like CARET, ignored the minus sign, and it turns out that all the numbers which were zeroed in CARET, where actually negative numbers in my original foci file. I tracked the problem back to the character used for the minus sign. When I created the excel file (from which I created the CSV foci file), I have sometimes cut and paste from PDF files or HTML files of the original articles. In some cases, the minus sign was a longer dash sign rather than a real minus sign. They look very similar but the wrong character is a slightly longer line if you look at it carefully. If you open the foci file I've sent before with Notepad (that is, if you use Windows) you will see what I mean. When I replaced these characters with real minus signs, the apparent bug was solved. I think this is a point to keep in mind because I am pretty sure many would cut and paste when creating large meta-analysis files (I have more than 100 points in the full file) rather than retype (which is also more prone to errors). Maybe CARET can be configured to detect this somehow and either report the problem or accept this other dash sign as minus. Many thanks for the quick response. Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 22, 2006 4:19 PM To: Leon Deouell Cc: 'Caret, SureFit,and SuMS software users' Subject: Re: [caret-users] using caret for a meta-analysis Hi Leon, This looks like a bug to me. I was able to replicate this behavior on my Caret 5.502 12/15/2006 Caret running RHEL. The ID readout for these foci were just fine (readout followed by corresponding line from foci file): Focus 2: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0) 2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch Focus 3: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0) 3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch But these foci had their x or y coordinate component zeroed out: Focus 4: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0) 4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch [Note from Donna: If left SFG, then wouldn't it be -20?) Focus 5: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0) 5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch Focus 6: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0) 6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch On 12/22/2006 03:26 AM, Leon Deouell wrote: Hi, I am finding something peculiar when looking at foci. To illustrate, I created a smaller file with only one study (foci file attached). I went through the following steps: 1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder 2. Opened the foci file test1study.foci 3. Projected the foci using Layers/Foci/Project Foci to PALS atlas (selecting 'project above surface [0.00]). The projected foci can be viewed in the attached figure coordinates.jpg Now I click on foci, and look the Identify Window. I find that for some, the values in 'Original Sterotaxic Positions' match the coordinates in the foci file. But for some (e.g., the one marked with a red ellipse in the figure) I get one of the coordinates set to zero. For example for this focus, I get: _ Focus 6: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): 41.0 0.0 6.0 Stereotaxic Position (FLIRT): 41.0 0.9 2.1 _ But focus 6 coordinates as specified in the foci file are actually [41, -75, 6] The same happens to a few others (but not all) foci. Sometimes it is the y coordinate that becomes zero, and sometimes the x coordinate. I verified that it is not something to do with the foci projection - the same results are obtained if I click the foci before projection. Any idea what I may be doing wr
RE: [caret-users] using caret for a meta-analysis
Ps. In case this helps any: This is the wrong characther: '-', and this is the right one: '-' . Using abs('-') in Matlab, the wrong one translates to 8211, while the correct minus sign translates to 45. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 22, 2006 4:19 PM To: Leon Deouell Cc: 'Caret, SureFit,and SuMS software users' Subject: Re: [caret-users] using caret for a meta-analysis Hi Leon, This looks like a bug to me. I was able to replicate this behavior on my Caret 5.502 12/15/2006 Caret running RHEL. The ID readout for these foci were just fine (readout followed by corresponding line from foci file): Focus 2: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0) 2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch Focus 3: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0) 3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch But these foci had their x or y coordinate component zeroed out: Focus 4: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0) 4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch [Note from Donna: If left SFG, then wouldn't it be -20?) Focus 5: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0) 5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch Focus 6: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0) 6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch On 12/22/2006 03:26 AM, Leon Deouell wrote: > Hi, > > I am finding something peculiar when looking at foci. To illustrate, I > created a smaller file with only one study (foci file attached). I went > through the following steps: > > 1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the > /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder > 2. Opened the foci file test1study.foci > 3. Projected the foci using Layers/Foci/Project Foci to PALS atlas > (selecting 'project above surface [0.00]). > > The projected foci can be viewed in the attached figure coordinates.jpg > > Now I click on foci, and look the Identify Window. I find that for some, the > values in 'Original Sterotaxic Positions' match the coordinates in the foci > file. But for some (e.g., the one marked with a red ellipse in the figure) I > get one of the coordinates set to zero. For example for this focus, I get: > > _ > Focus 6: MolholmEtAl05.pitch Class: pitch > Original Stereotaxic Position (AFNI): 41.0 0.0 6.0 > Stereotaxic Position (FLIRT): 41.0 0.9 2.1 > _ > > But focus 6 coordinates as specified in the foci file are > actually [41, -75, 6] > > The same happens to a few others (but not all) foci. Sometimes it is the y > coordinate that becomes zero, and sometimes the x coordinate. > > I verified that it is not something to do with the foci projection - the > same results are obtained if I click the foci before projection. > > Any idea what I may be doing wrong, or not interpreting correctly? > > Thanks, > > Leon > > > > > > > > -Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker > Sent: Friday, December 08, 2006 7:49 PM > To: Caret, SureFit, and SuMS software users > Subject: 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 > >> Th
RE: [caret-users] using caret for a meta-analysis
Dear Donna, Thanks to your critical eye, I found out what the problem is. You noted that for focus 4 the description is L Superior Frontal Gyrus but the x coordinate was 20 in your readout. However, in the foci file I've sent, the line actually says: 4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch I am not sure what you used to read the foci file, but it seems this software, like CARET, ignored the minus sign, and it turns out that all the numbers which were zeroed in CARET, where actually negative numbers in my original foci file. I tracked the problem back to the character used for the minus sign. When I created the excel file (from which I created the CSV foci file), I have sometimes cut and paste from PDF files or HTML files of the original articles. In some cases, the minus sign was a longer dash sign rather than a real minus sign. They look very similar but the wrong character is a slightly longer line if you look at it carefully. If you open the foci file I've sent before with Notepad (that is, if you use Windows) you will see what I mean. When I replaced these characters with real minus signs, the apparent bug was solved. I think this is a point to keep in mind because I am pretty sure many would cut and paste when creating large meta-analysis files (I have more than 100 points in the full file) rather than retype (which is also more prone to errors). Maybe CARET can be configured to detect this somehow and either report the problem or accept this other dash sign as minus. Many thanks for the quick response. Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 22, 2006 4:19 PM To: Leon Deouell Cc: 'Caret, SureFit,and SuMS software users' Subject: Re: [caret-users] using caret for a meta-analysis Hi Leon, This looks like a bug to me. I was able to replicate this behavior on my Caret 5.502 12/15/2006 Caret running RHEL. The ID readout for these foci were just fine (readout followed by corresponding line from foci file): Focus 2: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0) 2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch Focus 3: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0) 3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch But these foci had their x or y coordinate component zeroed out: Focus 4: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0) 4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch [Note from Donna: If left SFG, then wouldn't it be -20?) Focus 5: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0) 5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch Focus 6: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0) 6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch On 12/22/2006 03:26 AM, Leon Deouell wrote: > Hi, > > I am finding something peculiar when looking at foci. To illustrate, I > created a smaller file with only one study (foci file attached). I went > through the following steps: > > 1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the > /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder > 2. Opened the foci file test1study.foci > 3. Projected the foci using Layers/Foci/Project Foci to PALS atlas > (selecting 'project above surface [0.00]). > > The projected foci can be viewed in the attached figure coordinates.jpg > > Now I click on foci, and look the Identify Window. I find that for some, the > values in 'Original Sterotaxic Positions' match the coordinates in the foci > file. But for some (e.g., the one marked with a red ellipse in the figure) I > get one of the coordinates set to zero. For example for this focus, I get: > > _ > Focus 6: MolholmEtAl05.pitch Class: pitch > Original Stereotaxic Position (AFNI): 41.0 0.0 6.0 > Stereotaxic Position (FLIRT): 41.0 0.9 2.1 > _ > > But focus 6 coordinates as specified in the foci file are > actually [41, -75, 6] > > The same happens to a few others (but not all) foci. Sometimes it is the y > coordinate that becomes zero, and sometimes the x coordinate. > > I verified that it is not something to do with the foci projection - the > same results are obtained if I click the foci before projection. > > Any idea what I may be doing wrong, or not interpreting correctly? > > Thanks, > > Leon > > > > > > > > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTEC
Re: [caret-users] using caret for a meta-analysis
Hi Leon, This looks like a bug to me. I was able to replicate this behavior on my Caret 5.502 12/15/2006 Caret running RHEL. The ID readout for these foci were just fine (readout followed by corresponding line from foci file): Focus 2: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0) 2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch Focus 3: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0) 3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch But these foci had their x or y coordinate component zeroed out: Focus 4: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0) 4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch [Note from Donna: If left SFG, then wouldn't it be -20?) Focus 5: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0) 5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch Focus 6: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0) 6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch On 12/22/2006 03:26 AM, Leon Deouell wrote: Hi, I am finding something peculiar when looking at foci. To illustrate, I created a smaller file with only one study (foci file attached). I went through the following steps: 1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder 2. Opened the foci file test1study.foci 3. Projected the foci using Layers/Foci/Project Foci to PALS atlas (selecting 'project above surface [0.00]). The projected foci can be viewed in the attached figure coordinates.jpg Now I click on foci, and look the Identify Window. I find that for some, the values in 'Original Sterotaxic Positions' match the coordinates in the foci file. But for some (e.g., the one marked with a red ellipse in the figure) I get one of the coordinates set to zero. For example for this focus, I get: _ Focus 6: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): 41.0 0.0 6.0 Stereotaxic Position (FLIRT): 41.0 0.9 2.1 _ But focus 6 coordinates as specified in the foci file are actually [41, -75, 6] The same happens to a few others (but not all) foci. Sometimes it is the y coordinate that becomes zero, and sometimes the x coordinate. I verified that it is not something to do with the foci projection - the same results are obtained if I click the foci before projection. Any idea what I may be doing wrong, or not interpreting correctly? Thanks, Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 08, 2006 7:49 PM To: Caret, SureFit, and SuMS software users Subject: 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
RE: [caret-users] using caret for a meta-analysis
Hi, I am finding something peculiar when looking at foci. To illustrate, I created a smaller file with only one study (foci file attached). I went through the following steps: 1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder 2. Opened the foci file test1study.foci 3. Projected the foci using Layers/Foci/Project Foci to PALS atlas (selecting 'project above surface [0.00]). The projected foci can be viewed in the attached figure coordinates.jpg Now I click on foci, and look the Identify Window. I find that for some, the values in 'Original Sterotaxic Positions' match the coordinates in the foci file. But for some (e.g., the one marked with a red ellipse in the figure) I get one of the coordinates set to zero. For example for this focus, I get: _ Focus 6: MolholmEtAl05.pitch Class: pitch Original Stereotaxic Position (AFNI): 41.0 0.0 6.0 Stereotaxic Position (FLIRT): 41.0 0.9 2.1 _ But focus 6 coordinates as specified in the foci file are actually [41, -75, 6] The same happens to a few others (but not all) foci. Sometimes it is the y coordinate that becomes zero, and sometimes the x coordinate. I verified that it is not something to do with the foci projection - the same results are obtained if I click the foci before projection. Any idea what I may be doing wrong, or not interpreting correctly? Thanks, Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 08, 2006 7:49 PM To: Caret, SureFit, and SuMS software users Subject: 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:
Re: [caret-users] using caret for a meta-analysis
Leon, On Dec 9, 2006, at 7:59 AM, Leon Deouell wrote: Thanks again for your help. I am making nice progress. My questions now are: 1. Is it possible to see the foci on volume slices? It seems I can only see them on surface files. Yes - Use File: Open Data File: Open Foci File - Volumes (*.foci). This will open any valid foci file, and use whatever foci color file you have selected. Then select Display Control: Page Selection: Foci and toggle Show Volume Foci on. 2. Regardless of foci, when I switch to 'oblique' in a window displaying a volume, I loose the yoking option - clicking on the surface does not change the display in the volume window and vice versa. Is there a way to tilt the volume and remain "yoked"? My observations: Clicking on the surface does not move the cursor in the volume when viewing oblique slices, but it works for me in the reverse direction - clicking on the volume slice does highlight the corresponding node in the surface. Getting it to go in the reverse direction would be useful. Also, I just noticed that the surface slices don't display in the oblique volume slices even when selected using the O/L-Volume: Surface Outline option. However, John Harwell has a fair amount on his platter right now, so I'm not sure when he'll be able to get to it. David VE Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 08, 2006 7:49 PM To: Caret, SureFit, and SuMS software users Subject: 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:
RE: [caret-users] using caret for a meta-analysis
Thanks again for your help. I am making nice progress. My questions now are: 1. Is it possible to see the foci on volume slices? It seems I can only see them on surface files. 2. Regardless of foci, when I switch to 'oblique' in a window displaying a volume, I loose the yoking option - clicking on the surface does not change the display in the volume window and vice versa. Is there a way to tilt the volume and remain "yoked"? Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 08, 2006 7:49 PM To: Caret, SureFit, and SuMS software users Subject: 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
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 'layers>foci>map 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 Isra
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 'layers>foci>map 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 >
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 'layers>foci>map 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
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 'layers>foci>map 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, 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 'layers>foci>map 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
[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 'layers>foci>map 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