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): FAG Precentral_L 2001 FAD Precentral_R 2002 F1G Frontal_Sup_L 2101 ... VER8 Vermis_8 9150 VER9 Vermis_9 9160 VER10 Vermis_10 9170 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
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