[caret-users] posting reply for Donna
Dear Donna, I have uploaded the .spec file containing the "black" inflated, fiducial and spherical left hemisphere datasets. The file is a tar.gz format labelled "fordonna". Thank you again for your help. We are trying to deform the sulcal depth maps of subjects left hemispheres to the PALS atlas. Again, following spherical deformation, the left - but not right - fiducial, inflated and spherical hemispheres appear "black", as shown in the screen captures that are appended in jpg format. One important point is that when you click on the deformed lateral view, you get a medial view, so something is wrong here. There is a dorsal view of the deformed depth fiducial map; a dorsal view of the deformed sphere, and the medial view of the deformed inflated surface. As you will see, the appended and deformed flat maps look fine. Indeed, only one CLOSED topo file is loaded. The CLOSED topo file is: CLOSED Human.sphere_6.73730.topo The fiducial, inflated and spherical coord files are: deformed_Human.6.L.Fiducial.2006-02-13.64283.coord deformed_Human.6.L.Inflated.2006-02-13.64283.coord deformed_Human.6.L.SPHERE_ALIGN.2006-02-13.64283.coord We have tried troubleshooting this by performing this deform on other subjects left hemispheres, and the results are the same (so it cannot be due to a "bad" subjects dataset. We have also tried this on the right hemisphere using the same target atlas, so the atlas files are not corrupted. Finally, we have tried this on both the Linux and Mac platforms and we get the same results, i.e. "bad" left - but not right - hemisphere images. Best, Jason. Jason D. Connolly, PhD Center for Neural Science, New York University 6 Washington Place Room 875, New York, NY 10003 cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html <><><>
Re: [caret-users] posting
Jason, I'm getting ready to walk out the door (I get in around 7am), and a file named fordonna.tar.gz was just uploaded -- presumably from you. I looked at it, and with sane file selections, I don't see the black hole you described. Make sure you're using the topo that doesn't begin with deformed, but use the inflated and fiducial coords that are named like deformed*. I do see something funky with the topology, though, at the location indicated on the attached capture. I suspect it stems from your original surface, and has nothing to do with registration. Could you upload your original surface directory (using the same copy spec file, archive, upload approach), so I can be sure? It occurred to me: By black, you're not referring to the sulcal depth underlay, which makes deeper nodes appear darker, are you? You can turn this off, but we find it informative. On 04/19/2006 08:01 AM, Donna Dierker wrote: On 04/18/2006 03:50 PM, Jason D Connolly wrote: Dear David and Donna, I re-ran the left hemisphere deformation and I noticed that the deformed flat maps look alright. It is only the fiducial, inflated and spheres that are black. Make a "fordonna" subdirectory and use Copy Spec file to copy the spec file you are viewing to that subdirectory. Then, create a zip or tar.gz archive of that subdirectory and upload it here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi I need to know exactly which CLOSED topo and fiducial, inflated, and spherical coord files you have loaded. Make sure only one CLOSED topo file is loaded. I also noticed that when the spherical deformation is run, the central sulcus appears on the right side and the medial wall on the left during warping. This is normal. During registration, left hemispheres are flipped and treated as if they were right hemispheres. This is normal behavior and causes no problems. Following deformation there are 2 sets of borders that appear on the spheres the "left" set and also concurrently a "right" (or perhaps target) set. The two sets are overlaid on the spheres. Sounds to me like you have the target border file Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.SPHERE.border selected. I'm still in the dark as to what your goal is -- the type of data you're trying to register to PALS (e.g., sulcal depth? functional data?). Jason. Jason D. Connolly, PhD Center for Neural Science, New York University 6 Washington Place Room 875, New York, NY 10003 cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html ___ 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] help needed
Hi Binyam, That border/borderproj files in that spec file don't include the Core6 landmarks. If you really want them, you could download this borderproj and bordercolor file: Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.PALS-B12-SPHERE.borderproj http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6334050 ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057515 Use File: Open Data File to load the bordercolor first, then the borderproj file. But if you're trying to orient yourself to the different sulci, then another way of doing this might be to view your ROI paint regions, but also have the def_to_PALS_B12.LR_Human.colin.Cerebral.L.COMPOSITE.clean.71785.paint and Human.Cerebral.COMPOSITE_OrbFrontClusters.areacolor files loaded. Then, when you click on a node or voxel in your ROI, the ID window will spit out lots of information about that node, e.g.: Node 38255 Main Window Inflated XYZ: 15.0824, -7.7470, 68.5119 Distance: 32.0371 View Window 2 Inflated XYZ: 15.0824, -7.7470, 68.5119 Distance: 32.0371 Section: 80 Lat/Lon PALS-B12.LR Latitude-Longitude: 2.1453 105.0355 Lat/Lon deformed Human Colin LEFT: -11.2868 102.4004 Atlas Lat/Lon deformed Human Colin LEFT: -11.2868 102.4004 Paint: LOBE.FRONTAL SUL SUL.CeS MOTOR ??? ??? BROD.4 LANDMARK.Brodmann_4 Shape: -15.4029 -0.0788 The Paint: ... SUL.CeS ... tells you this node is in the central sulcus. The comment (click on ? button to the right of the Paint radio buttons on the D/C: Overlay/Underlay - Surface menu) for the deformed Sulcal ID - Human.colin.L column lists the abbreviations for the sulci. On 04/19/2006 10:16 AM, Binyam Nardos wrote: Hi Donna, Please see inline responses. Thanks for your help, Binyam -Original Message- From: [EMAIL PROTECTED] on behalf of Donna Dierker Sent: Wed 4/19/2006 8:35 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] help needed Hi Binyam, See inline responses below. On 04/18/2006 06:28 PM, Binyam Nardos wrote: Dear Caret support, Just started using Caret and I have what might be some elementary questions for you. I have been trying to make the central sulcus landmark appear in my fiducial and inflated surfaces that I've mapped regions of interest on. However, I can't seem to be able to get it to show, I tried loading all the border data files that I could find in the PALS folder but the only thing I can get to show up are the lobe markers(the border files for the central sulcus marker do show up in the display control window so I'm thinking they are loaded); I also tried playing with the border colors(specifically those for the central sulcus marker) but still couldn't get it. Which spec file are you using? If you got it from sumsdb.wustl.edu, do you know the directory or archive ID, so I can find it quickly? If not, then perhaps just the name of the spec file will help. I assume you're using a publicly available PALS_B12 dataset, rather than a surface you reconstructed and registered of your own. Here's the spec file that I am using: Human.PALS_B12.LEFT_HEM.with-COLIN-DATA.73730 and it's in the PALS_Left_Atlas directory that I got from the sums db. I'm trying out the suggestion you made below. One more question: I have a volume anatomy file that I've loaded regions of interest as functional volume files. They show up fine but I was wondering if there was a way to make each individual region appear in a different color. Now i've been able to do this while mapping regions on a fiducial surface by defining a different area color for each region, is the same thing possible in the volume anatomy view.? There is a way to do this -- at least if your paint/ROI intensities/indices are ordered sequentially (i.e., 1, 2, 3, ...). If not, then I'm not sure how to do this. Back on 9/2005, a user wanted to map the AAL ROIs to PALS, but it's intensity-to-parcel scheme looked like this (116 labels): FAGPrecentral_L2001 FADPrecentral_R2002 F1GFrontal_Sup_L2101 ... VER8Vermis_89150 VER9Vermis_99160 VER10Vermis_109170 The trouble is that the paint index to paint name mapping is stored in the AFNI .HEAD file like this: type = string-attribute name = LUT_NAMES count = 423 '???~???_not_used~GYRAL~SUL.STS~SUL.AS~SUL.SF~SUL.ITS~SUL.PoCeS~SUL.PoSubCeS~SUL.CeS~SUL.IPrCeS~SUL.pITS~SUL~SUL.IFS~SUL.IPS~SUL.AOS~SUL.OTS~CENTRAL~SUL.intFS~SUL.SPrCeS~SUL.FOS~SUL.MFS~SUL.TOrbS~SUL.LOS~SUL.FMS~SUL.SFS~SUL.CoS~SUL.TOS~SUL.SupPS~SUL.RhS~CALCARINE~MEDIAL.WALL~SUL.CaSd~SUL.OrbS~SUL.HF~SUL.CaSv~SUL.POS~SUL.CiSmr~SUL.CiS~SUL.SSS~SUL.SubPS~SUL.OlfS~SUL.ILS~SUL.SRS~SUL.ISS~SUL.MPrCeS~SUL.PaCeS~SUL.IRS~SUL.LuS~ The ordinal position of the name corresponds to the intensity (first is intensity=1; second is intensity=2, and so on). But for the AAL volume, we'd need 2000 bogus names just to get to the first real AA
RE: [caret-users] help needed
Hi Donna, I've managed to solve the second problem i.e.: > One more question: I have a volume anatomy file that I've loaded > regions of interest as functional volume files. They show up fine but > I was wondering if there was a way to make each individual region > appear in a different color. Now i've been able to do this while > mapping regions on a fiducial surface by defining a different area > color for each region, is the same thing possible in the volume > anatomy view.? What I did to was load my regions of interest as a volume paint file instead of a functional volume file like I had initially done. I can now define different colors for each individual region. Binyam -Original Message- From: [EMAIL PROTECTED] on behalf of Binyam Nardos Sent: Wed 4/19/2006 10:16 AM To: Caret, SureFit, and SuMS software users Subject: RE: [caret-users] help needed Hi Donna, Please see inline responses. Thanks for your help, Binyam -Original Message- From: [EMAIL PROTECTED] on behalf of Donna Dierker Sent: Wed 4/19/2006 8:35 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] help needed Hi Binyam, See inline responses below. On 04/18/2006 06:28 PM, Binyam Nardos wrote: > > Dear Caret support, > Just started using Caret and I have what might be some elementary > questions for you. I have been trying to make the central sulcus > landmark appear in my fiducial and inflated surfaces that I've mapped > regions of interest on. However, I can't seem to be able to get it to > show, I tried loading all the border data files that I could find in > the PALS folder but the only thing I can get to show up are the lobe > markers(the border files for the central sulcus marker do show up in > the display control window so I'm thinking they are loaded); I also > tried playing with the border colors(specifically those for the > central sulcus marker) but still couldn't get it. > Which spec file are you using? If you got it from sumsdb.wustl.edu, do you know the directory or archive ID, so I can find it quickly? If not, then perhaps just the name of the spec file will help. I assume you're using a publicly available PALS_B12 dataset, rather than a surface you reconstructed and registered of your own. Here's the spec file that I am using: Human.PALS_B12.LEFT_HEM.with-COLIN-DATA.73730 and it's in the PALS_Left_Atlas directory that I got from the sums db. I'm trying out the suggestion you made below. > > One more question: I have a volume anatomy file that I've loaded > regions of interest as functional volume files. They show up fine but > I was wondering if there was a way to make each individual region > appear in a different color. Now i've been able to do this while > mapping regions on a fiducial surface by defining a different area > color for each region, is the same thing possible in the volume > anatomy view.? > There is a way to do this -- at least if your paint/ROI intensities/indices are ordered sequentially (i.e., 1, 2, 3, ...). If not, then I'm not sure how to do this. Back on 9/2005, a user wanted to map the AAL ROIs to PALS, but it's intensity-to-parcel scheme looked like this (116 labels): FAGPrecentral_L2001 FADPrecentral_R2002 F1GFrontal_Sup_L2101 ... VER8Vermis_89150 VER9Vermis_99160 VER10Vermis_109170 The trouble is that the paint index to paint name mapping is stored in the AFNI .HEAD file like this: type = string-attribute name = LUT_NAMES count = 423 '???~???_not_used~GYRAL~SUL.STS~SUL.AS~SUL.SF~SUL.ITS~SUL.PoCeS~SUL.PoSubCeS~SUL.CeS~SUL.IPrCeS~SUL.pITS~SUL~SUL.IFS~SUL.IPS~SUL.AOS~SUL.OTS~CENTRAL~SUL.intFS~SUL.SPrCeS~SUL.FOS~SUL.MFS~SUL.TOrbS~SUL.LOS~SUL.FMS~SUL.SFS~SUL.CoS~SUL.TOS~SUL.SupPS~SUL.RhS~CALCARINE~MEDIAL.WALL~SUL.CaSd~SUL.OrbS~SUL.HF~SUL.CaSv~SUL.POS~SUL.CiSmr~SUL.CiS~SUL.SSS~SUL.SubPS~SUL.OlfS~SUL.ILS~SUL.SRS~SUL.ISS~SUL.MPrCeS~SUL.PaCeS~SUL.IRS~SUL.LuS~ The ordinal position of the name corresponds to the intensity (first is intensity=1; second is intensity=2, and so on). But for the AAL volume, we'd need 2000 bogus names just to get to the first real AAL label, whose intensity is 2001. I'm not sure how you get this info into Caret using the GUI; in the past, I've simply edited the .HEAD file with a text editor (I know, naughty Donna, but the AFNI police probably already have warrants out for us for using a non-standard attribute such as LUT_NAMES;-). > > Much appreciated, > Binyam Nardos > > > >___ >caret-users mailing list >caret-users@brainvis.wustl.edu >http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) ___ caret-users mailing list caret-users@bra
RE: [caret-users] help needed
Hi Donna, Please see inline responses. Thanks for your help, Binyam -Original Message- From: [EMAIL PROTECTED] on behalf of Donna Dierker Sent: Wed 4/19/2006 8:35 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] help needed Hi Binyam, See inline responses below. On 04/18/2006 06:28 PM, Binyam Nardos wrote: > > Dear Caret support, > Just started using Caret and I have what might be some elementary > questions for you. I have been trying to make the central sulcus > landmark appear in my fiducial and inflated surfaces that I've mapped > regions of interest on. However, I can't seem to be able to get it to > show, I tried loading all the border data files that I could find in > the PALS folder but the only thing I can get to show up are the lobe > markers(the border files for the central sulcus marker do show up in > the display control window so I'm thinking they are loaded); I also > tried playing with the border colors(specifically those for the > central sulcus marker) but still couldn't get it. > Which spec file are you using? If you got it from sumsdb.wustl.edu, do you know the directory or archive ID, so I can find it quickly? If not, then perhaps just the name of the spec file will help. I assume you're using a publicly available PALS_B12 dataset, rather than a surface you reconstructed and registered of your own. Here's the spec file that I am using: Human.PALS_B12.LEFT_HEM.with-COLIN-DATA.73730 and it's in the PALS_Left_Atlas directory that I got from the sums db. I'm trying out the suggestion you made below. > > One more question: I have a volume anatomy file that I've loaded > regions of interest as functional volume files. They show up fine but > I was wondering if there was a way to make each individual region > appear in a different color. Now i've been able to do this while > mapping regions on a fiducial surface by defining a different area > color for each region, is the same thing possible in the volume > anatomy view.? > There is a way to do this -- at least if your paint/ROI intensities/indices are ordered sequentially (i.e., 1, 2, 3, ...). If not, then I'm not sure how to do this. Back on 9/2005, a user wanted to map the AAL ROIs to PALS, but it's intensity-to-parcel scheme looked like this (116 labels): FAGPrecentral_L2001 FADPrecentral_R2002 F1GFrontal_Sup_L2101 ... VER8Vermis_89150 VER9Vermis_99160 VER10Vermis_109170 The trouble is that the paint index to paint name mapping is stored in the AFNI .HEAD file like this: type = string-attribute name = LUT_NAMES count = 423 '???~???_not_used~GYRAL~SUL.STS~SUL.AS~SUL.SF~SUL.ITS~SUL.PoCeS~SUL.PoSubCeS~SUL.CeS~SUL.IPrCeS~SUL.pITS~SUL~SUL.IFS~SUL.IPS~SUL.AOS~SUL.OTS~CENTRAL~SUL.intFS~SUL.SPrCeS~SUL.FOS~SUL.MFS~SUL.TOrbS~SUL.LOS~SUL.FMS~SUL.SFS~SUL.CoS~SUL.TOS~SUL.SupPS~SUL.RhS~CALCARINE~MEDIAL.WALL~SUL.CaSd~SUL.OrbS~SUL.HF~SUL.CaSv~SUL.POS~SUL.CiSmr~SUL.CiS~SUL.SSS~SUL.SubPS~SUL.OlfS~SUL.ILS~SUL.SRS~SUL.ISS~SUL.MPrCeS~SUL.PaCeS~SUL.IRS~SUL.LuS~ The ordinal position of the name corresponds to the intensity (first is intensity=1; second is intensity=2, and so on). But for the AAL volume, we'd need 2000 bogus names just to get to the first real AAL label, whose intensity is 2001. I'm not sure how you get this info into Caret using the GUI; in the past, I've simply edited the .HEAD file with a text editor (I know, naughty Donna, but the AFNI police probably already have warrants out for us for using a non-standard attribute such as LUT_NAMES;-). > > Much appreciated, > Binyam Nardos > > > >___ >caret-users mailing list >caret-users@brainvis.wustl.edu >http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users <>
Re: [caret-users] help needed
Hi Binyam, See inline responses below. On 04/18/2006 06:28 PM, Binyam Nardos wrote: Dear Caret support, Just started using Caret and I have what might be some elementary questions for you. I have been trying to make the central sulcus landmark appear in my fiducial and inflated surfaces that I've mapped regions of interest on. However, I can't seem to be able to get it to show, I tried loading all the border data files that I could find in the PALS folder but the only thing I can get to show up are the lobe markers(the border files for the central sulcus marker do show up in the display control window so I'm thinking they are loaded); I also tried playing with the border colors(specifically those for the central sulcus marker) but still couldn't get it. Which spec file are you using? If you got it from sumsdb.wustl.edu, do you know the directory or archive ID, so I can find it quickly? If not, then perhaps just the name of the spec file will help. I assume you're using a publicly available PALS_B12 dataset, rather than a surface you reconstructed and registered of your own. One more question: I have a volume anatomy file that I've loaded regions of interest as functional volume files. They show up fine but I was wondering if there was a way to make each individual region appear in a different color. Now i've been able to do this while mapping regions on a fiducial surface by defining a different area color for each region, is the same thing possible in the volume anatomy view.? There is a way to do this -- at least if your paint/ROI intensities/indices are ordered sequentially (i.e., 1, 2, 3, ...). If not, then I'm not sure how to do this. Back on 9/2005, a user wanted to map the AAL ROIs to PALS, but it's intensity-to-parcel scheme looked like this (116 labels): FAGPrecentral_L2001 FADPrecentral_R2002 F1GFrontal_Sup_L2101 ... VER8Vermis_89150 VER9Vermis_99160 VER10Vermis_109170 The trouble is that the paint index to paint name mapping is stored in the AFNI .HEAD file like this: type = string-attribute name = LUT_NAMES count = 423 '???~???_not_used~GYRAL~SUL.STS~SUL.AS~SUL.SF~SUL.ITS~SUL.PoCeS~SUL.PoSubCeS~SUL.CeS~SUL.IPrCeS~SUL.pITS~SUL~SUL.IFS~SUL.IPS~SUL.AOS~SUL.OTS~CENTRAL~SUL.intFS~SUL.SPrCeS~SUL.FOS~SUL.MFS~SUL.TOrbS~SUL.LOS~SUL.FMS~SUL.SFS~SUL.CoS~SUL.TOS~SUL.SupPS~SUL.RhS~CALCARINE~MEDIAL.WALL~SUL.CaSd~SUL.OrbS~SUL.HF~SUL.CaSv~SUL.POS~SUL.CiSmr~SUL.CiS~SUL.SSS~SUL.SubPS~SUL.OlfS~SUL.ILS~SUL.SRS~SUL.ISS~SUL.MPrCeS~SUL.PaCeS~SUL.IRS~SUL.LuS~ The ordinal position of the name corresponds to the intensity (first is intensity=1; second is intensity=2, and so on). But for the AAL volume, we'd need 2000 bogus names just to get to the first real AAL label, whose intensity is 2001. I'm not sure how you get this info into Caret using the GUI; in the past, I've simply edited the .HEAD file with a text editor (I know, naughty Donna, but the AFNI police probably already have warrants out for us for using a non-standard attribute such as LUT_NAMES;-). Much appreciated, Binyam Nardos ___ 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] posting
On 04/18/2006 03:50 PM, Jason D Connolly wrote: Dear David and Donna, I re-ran the left hemisphere deformation and I noticed that the deformed flat maps look alright. It is only the fiducial, inflated and spheres that are black. Make a "fordonna" subdirectory and use Copy Spec file to copy the spec file you are viewing to that subdirectory. Then, create a zip or tar.gz archive of that subdirectory and upload it here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi I need to know exactly which CLOSED topo and fiducial, inflated, and spherical coord files you have loaded. Make sure only one CLOSED topo file is loaded. I also noticed that when the spherical deformation is run, the central sulcus appears on the right side and the medial wall on the left during warping. This is normal. During registration, left hemispheres are flipped and treated as if they were right hemispheres. This is normal behavior and causes no problems. Following deformation there are 2 sets of borders that appear on the spheres the "left" set and also concurrently a "right" (or perhaps target) set. The two sets are overlaid on the spheres. Sounds to me like you have the target border file Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.SPHERE.border selected. I'm still in the dark as to what your goal is -- the type of data you're trying to register to PALS (e.g., sulcal depth? functional data?). Jason. Jason D. Connolly, PhD Center for Neural Science, New York University 6 Washington Place Room 875, New York, NY 10003 cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html ___ 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.)
