I don't think we have figured out how to make FreeSurfer data run with oblique sforms line up with volume data in Caret. I have avoided this issue by always removing the oblique sforms before running FreeSurfer. In theory, it must be possible to fix, however the different software handle the oblique sforms differently. I'll have to defer to others in the lab (Tim) on if this is solvable however. The issue is that the offset between the surfaces and volume (FreeSurfer's c_ras) no longer causes the surfaces and volumes to align in Caret if you gave FreeSurfer data with oblique sforms.
I think the upload site is: http://pulvinar.wustl.edu/cgi-bin/upload.cgi Peace, Matt. On 5/7/13 9:48 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 5 >tel. 01 44 32 29 92 > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
