To dump the header info, there is fslhd from fsl, or wb_command -nifti-information (part of connectome workbench), or 3dinfo (from afni). caret5 is allergic to obliques, and may not have a utility to tell you about them.
wb_command can handle oblique volumes, so if you have a suitable volume space to resample them into (or create one with caret_command -volume-create), you can resample the T1 and T2, and then use those. Alternatively, you could fake the header sforms to be plumb (fsledithd?), apply an equivalent transform to the surfaces, and use those. Or, you could do the equivalent of the myelin mapping method using wb_command operations, since it doesn't object to oblique volumes. Tim On Tue, Apr 30, 2013 at 10:16 AM, Irene Altarelli <[email protected]>wrote: > Dear Caret experts, > > I'd like to use the myelin mapping processing stream. I have processed > my T1 scans with Freesurfer 5.0 some time ago, finely correcting the > segmentation for a number of subjects (these are children). > > From what I have read from the documentation it appears that oblique > s/qforms might be creating some problems. I am afraid that I have them > in my already processed T1s, given the output of mri_info. > > I also got two versions of the T2 sequence from the scanner, one > apparently being somewhat filtered. > > May I ask you to have a look at these images and their headers and give > me some advice on how to proceed? I can upload them wherever you think > is easy to access. > > Thank you very much in advance. > Best, > Irene > > > > > -- > > Irene Altarelli, PhD student > Laboratoire de Sciences Cognitives et Psycholinguistique > Ecole Normale Supérieure > 29, rue d'Ulm > 75230 Paris Cedex 05 > tel. 01 44 32 29 92 > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users >
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