Yes, I use the CARET_TUTORIAL_SEPT06/MAPPNING_PROCEDURES files, and load the Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file.
I think I got the hang of it. The break through was, after creating the metric file load one of the predefined scenes before trying to open my metric file. In this way it didn't complain anymore about different number of nodes. If I understand it right if I want now to see the activation on a pial surface I should just open the coord file and add it to my template spec file. Do you know where I could find this? I think it should also be something between pial and fiducial. Also, L and R are overlaid wrong, what SPM reports as left, I see it on the right hemisphere in Caret. How can this be changed? Thanks, Julian -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Wednesday, March 07, 2007 4:05 PM To: Caret, SureFit, and SuMS software users Subject: [BULK] Re: [caret-users] Map SPM volume Importance: Low Hi Julian, When mapping to atlas, are you selecting a spec file created from this dataset: CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu/sums/directory.do?id=6585200 ... using steps as described in Section 5.1 of this tutorial: Caret_Tutorial_Oct06.pdf http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379 It's tough to see how you could get this error under those circumstances, since the files in that spec file (or derivative thereof) all have the same 73730 standard mesh. While this spec won't have a pial surface, it will have left and right versions of the following configurations: PALS_B12 average fiducial inflated very inflated flat Since you're using SPM2, I'd suggest replacing the average fiducial coord files with these files: Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord To do so, after opening Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File: Open Data File: and select Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. Repeat for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. Then, select Toolbar: Spec and use the X buttons to delete these versions, which are similar but not as optimal as the SPM2 versions in your case: Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord Both the SPM2 and FLIRT versions are in mni152 space, but the contributing PALS_B12 anatomicals were normalized using SPM2 for the SPM2 versions, while FSL's flirt (affine only) was used to normalize the FLIRT versions. Donna On 03/07/2007 08:33 AM, Julianm Macoveanu wrote: > > Hi guys, > > I need some help with basic stuff. I just want to use Caret to > visualize my SPM2 activations on inflated/Fiducial surfaces. So I have > the normalized volume file to start with. > > > > I have opened a spec file from the Caret tutorial, use the map volume > to surface function, choose my volume, then Map to spec file with > atlas (and without). I have also tried not to open any spec file to > begin with, and then just open the one I chose as output during the > mapping procedure > > > > As space I tried the SPM2, as this is the kind of volume I have (but > also 711-sc). > > > > After the metric file is generated, I just try to open it, but I get > the error that my metric file contains different number of nodes. > > > > What I would like to have is a spec file that have all different > surfaces (including pial and multi-fiducial which I could not find in > any examples of spec files) and then just create metric files from my > SPM volumes in order to visualize the activations. > > > > Cheers, > > Julian > > > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
