Hi Alex,1) The fiducial surface is not a good configuration for drawing borders. The terrain is too uneven. Depending on how many borders you are drawing, I would recommend one of these alternate strategies:
* Import the Freesurfer inflated surface and use it for this purpose. * Generate an inflated surface from the fiducial in Caret. * Flatten the hemisphere and draw on the flat surface.Note that the depth can be viewed on any configuration; you can draw on one surface, but compute surface area on another surface.
2) The Reassign nodes ... checkbox is intended for purposes like yours (if I understand your goal properly). For example, if you want to draw a border just around the anterior cinculate, but you only want the sulcus (buried cortex) -- not the nearby gyral regions -- then using this feature reassigns only nodes with geography = SUL to the name of whatever border you are drawing, let's say CiS. The attached captures show the Draw Borders settings and the painted region (just the anterior portion of the CiS, since I was lazy). Notice how I could be kind of sloppy while drawing the border (i.e., didn't have to trace along the edges of the geography paint SUL region), since only the SUL nodes get reassigned -- not the gyral nodes. So your resulting ROI area report will include area on the sulcal CiS nodes only.
3) I'll reply to the script question off-list. Donna On 02/13/2006 06:03 PM, Fornito, Alexander wrote:
Hi Donna, I'm actually drawing on the fiducial surface, so I choose 3D and closed. I check 'assign paint identifiers to nodes within border' And name the paint column Sul I don't check reassign nodes with because I don't know what this is for. Also, how and when do I run the script for adding the hem flag to the spec file? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -----Original Message----- From: [EMAIL PROTECTED] on behalf of Donna Hanlon Sent: Tue 14/02/2006 9:19 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Viewing ROIs On 02/13/2006 03:37 PM, Fornito, Alexander wrote:Ok, I had a look under attributes and I saw the ROI I created, so I assume this is correct. I tried to create a new ROi under the attributes > area color tab named ???. This got rid of the > WARNING: Paint names with no corresponding area colors:??? in the shell but it highlighted the rest of the brain (outside the ROI).I could still not visualize my ROI.It's safe to just ignore this warning: Paint names with no corresponding area colors:???I've also noticed that in cases where I can visualize the ROI, only exposed nodes are highlihted; nodes in the sulcal depths are not highlighted.Let's clarify your Draw Borders settings: Type: closed Dimension: 2D (i.e., you're drawing on a flat map) Closed border assignment: Surfaces Nodes: Assign Paint Identifiers to nodes within border checkbox is selected Paint Column: -- what are you using here? Reassign nodes with -- is this checked, and if so, what is selected?I created my surfaces using the command line utlity.Maybe I've done something wrong? My commands are below. I've also noticed that alothough my left surface comes up in the correct orientation, Caret confuses the medial and lateral surfaces for my right hemispheres; when I press L it takes me to the medial view, and when I press M it takes me to the lateral view. All other viewing conrtols seem to be correct.Adding a line like this to your spec file will solve this problem: hem_flag rightThis looks good, except I have been using "left" instead of "LEFT"; also, I'm using smoothwm instead of white, but I don't have a strong preference on this.LEFT: /usr/local/caret/bin/caret_file_convert -sc -is FSS lh.white.asc -os CARET 1000001.lh.white.coord 1000001.lh.closed.topo RAW CLOSED -spec 1000001.lh.spec -hem LEFTI need to check with John Harwell on this; I'm guessing the origin is a coordinate -- not a voxel index. I'm trying to get clarification from some folks on the AFNI message board:/usr/local/caret/bin/caret_file_convert -sc -is FSS lh.pial.asc -os CARET 1000001.lh.pial.coord 1000001.lh.closed.topo RAW CLOSED -spec 1000001.lh.spec -hem LEFT /usr/local/caret/bin/caret_command -surface-average 1000001.lh.FIDUCIAL.coord 1000001.lh.white.coord 1000001.lh.pial.coord /usr/local/caret/bin/caret_command -volume-create 256 256 256 -128 -128 -128 1 1 1 RIA 1000001_segvol.hdrhttp://afni.nimh.nih.gov/afni/community/board/read.php?f=1&i=9128&t=9128 But this should get you in the ballpark./usr/local/caret/bin/caret_command -surface-to-segmentation-volume 1000001.lh.FIDUCIAL.coord 1000001.lh.closed.topo 1000001_segvol.hdr /usr/local/caret/bin/caret_command -surface-identify-sulci 1000001.lh.spec left 1000001_segvol.hdr 1000001.lh.closed.topo 1000001.lh.FIDUCIAL.coord 1000001.lh.FIDUCIAL.coord RIGHT: /usr/local/caret/bin/caret_file_convert -sc -is FSS rh.white.asc -os CARET 1000001.rh.white.coord 1000001.rh.closed.topo RAW CLOSED -spec 1000001.rh.spec -hem RIGHT /usr/local/caret/bin/caret_file_convert -sc -is FSS rh.pial.asc -os CARET 1000001.rh.pial.coord 1000001.rh.closed.topo RAW CLOSED -spec 1000001.rh.spec -hem RIGHT /usr/local/caret/bin/caret_command -surface-average 1000001.rh.FIDUCIAL.coord 1000001.rh.white.coord 1000001.rh.pial.coord /usr/local/caret/bin/caret_command -volume-create 256 256 256 -128 -128 -128 1 1 1 RIA 1000001_segvol.hdr /usr/local/caret/bin/caret_command -surface-to-segmentation-volume 1000001.rh.FIDUCIAL.coord 1000001.rh.closed.topo 1000001_segvol.hdr /usr/local/caret/bin/caret_command -surface-identify-sulci 1000001.rh.spec right 1000001_segvol.hdr 1000001.rh.closed.topo 1000001.rh.FIDUCIAL.coord 1000001.rh.FIDUCIAL.coord Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -----Original Message----- From: [EMAIL PROTECTED] on behalf of John Harwell Sent: Tue 14/02/2006 5:43 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Viewing ROIs On Feb 13, 2006, at 1:13 AM, Fornito, Alexander wrote:Hi,I seem to be able to view manually drawn ROIs with variable consistency, and its causing me a bit of confusion. For example, in the right hemisphere of one of my subjects, I draw the ROI using Layers>Borders>Draw Border. I then save the area color file and paint file, and when I check the paint row in the D/C, I can see the ROI I drew. If I repeat this process in the left hemisphere, I can't see it and the shell I'm running Caret from returns the message:WARNING: Paint names with no corresponding area colors: ???I'm not sure why the same process would work for one hemisphere and not the other. Note this also happens if I exit Caret and try to re- load the area color and paint files.Any help is much appreciated. Thanks, AlexAlex,When you assign a paint area, nodes that have not been identified by the user are given the name "???" which implies that the nodes' identities are unknown. The WARNING message is produced because there is no color available for nodes with identity "???". You can eliminate this message by adding a color for "???" by selecting Edit from the Attributes:Area Colors menu. The lack of a color for "???"should not affect the drawing of ROIs.On the Surface:Region of Interest Dialog, make sure that you see nodes appear in green after pressing the Select Nodes pushbutton to select your region. When assigning the paint identifier, be sure to provide a name for the nodes before pressing the Assign pushbutton.---------------------------------------------------------- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave. Box 8108 St. Louis, MO 63110 USA _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ------------------------------------------------------------------------ _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users_______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
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