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 right >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 LEFT > > This 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. >/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.hdr > > I 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: http://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, >>Alex >> >> >> > >Alex, > >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
