Go here: http://sumsdb.wustl.edu/sums/directory.do?id=6585200&dir_name=CARET_TUTORIAL_SEPT-06
Download the zip file. Extract it. Use this spec file: PALS_B12.RIGHT.STANDARD-SCENES.73730.spec It doesn't have the SPM5 fiducial in it, but you can load that directly by opening the spec file and using File: Open Data file: and navigating to the Caret distribution directory, data_files/fmri_mapping_files/Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM5.clean.73730.coord. Map to the PALS SPM5 Right atlas only, and see if you get better results. Donna On 04/13/2011 09:54 AM, Xiaozhen You wrote: > Hi Donna, > Is there a way I can find the specific right hemishpere atlas (instead > of both hemisphere) for SPM5 space? > Thank you! > Best, > > > On Tue, Apr 12, 2011 at 6:00 PM, Xiaozhen You <[email protected] > <mailto:[email protected]>> wrote: > > Sorry to hear that you are sick Donna. and thank you for replying > promptly! > The problem is I was using SPM8 to normalize my data into their > EPI template, and the spec i found recommended by caret was > "the Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec" or > MGH group was > " PALS.B12.BOTH-HEMS.For-Stereotaxic-foci-analyses.73730.spec". > For both I tried, and the space I chose SPM5, as there is no SPM8. > But weirdly, for atlas under SPM5, there is only left > human.pals.multi.fidmap.Left.hemisphere.73730, but no > corresponding human.pals.multi.fidmap.right.hemisphere.73730... > > Do you think the choices I made were reasonable, and do you know > where I can find the right hemisphere atlas for SPM5 that > associate with a specific spec file good for fmri mapping using SPM8? > > Thank you again and hope you feel better! > Best, > > On Tue, Apr 12, 2011 at 5:38 PM, Donna Dierker > <[email protected] <mailto:[email protected]>> wrote: > > I am at home sick today, so it's not easy for me to replicate > your results. > > But when I have trouble like this, I revert to using single > hem spec files > -- RIGHT or LEFT. Map only to one or the other. Do them one > at a time. > See if it helps. > > > Dear Caret experts, > > I've been using Caret to map the connectivity results, and > just notice > > that > > the patterns always look the same on both hemisphere, even > when I know > > there > > is no DLPFC on the left hemisphere but only on right > hemisphere, (which is > > validated by overlaying them on MRICron, but it just look > the same on > > CARET! > > Here is what I did: > > 1. generate NIFTI format filr for thresholded spmT.hdr file > > 2. menu-attribute- map volume to surface-metric(function) > surface > > data->add > > volumes from disk->map spec file with atlas->choose " > PALS.B12.*BOTH*-* > > HEMS.For-*Stereotaxic-foci-analyses.73730.spec", space " > SPM5" (as I > > processed everything in SPM8), atlas " > > > > PALS.B12.*BOTH*-*HEMS.For-*Stereotaxic-foci-analyses.73730.spec".->enclosing > > voxel. > > 3. view results, I loaded the metric and spec file, primary > overlay > > ("metric"), then model I chose > > > > "fiducial.human.pals_B12.Left.Average.B1-12.fiducial_moritotal_clean.73730.coord". > > Then change the model to > > > > "fiducial.human.pals_B12.right.Average.B1-12.fiducial_moritotal_clean.73730.coord". > > > > They look the same, even with different metric setting ( > like threshold > > selection) > > Could you help me figure out what did I do wrong? Thank you! > > Best, > > > > -- > > Xiaozhen You, PhD > > Developmental Cognitive Neuroscience Lab > > Georgetown University > > 401 White-Gravenor > > 3700 O Street, NW > > Washington DC 20057 > > [email protected] <mailto:[email protected]> > > 202-687-9133 <tel:202-687-9133>/ > > 202-687-8223 <tel:202-687-8223> > > _______________________________________________ > > caret-users mailing list > > [email protected] > <mailto:[email protected]> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > [email protected] > <mailto:[email protected]> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > -- > Xiaozhen You, PhD > Developmental Cognitive Neuroscience Lab > Georgetown University > 401 White-Gravenor > 3700 O Street, NW > Washington DC 20057 > [email protected] <mailto:[email protected]> > 202-687-9133 <tel:202-687-9133>/ > 202-687-8223 <tel:202-687-8223> > > > > > -- > Xiaozhen You, PhD > Developmental Cognitive Neuroscience Lab > Georgetown University > 401 White-Gravenor > 3700 O Street, NW > Washington DC 20057 > [email protected] <mailto:[email protected]> > 202-687-9133/ > 202-687-8223 > ------------------------------------------------------------------------ > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
