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Hi Elisa Can you send me the following files: - tensor prior to vecreg - tensor post-vecreg - fnirt warpfield You can use the link below to upload these files: https://oxfile.ox.ac.uk/oxfile/work/extBox?id=185383653329207897 Cheers Saad On 16 Oct 2014, at 16:21, Elisa Scaccianoce <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi everybody! I need to perform DTI analysis in a 2 mm isotropic standard space. I registered the FA map with FNIRT, using a resampled version of the FMRIB58_FA (2 mm iso) as reference, instead of the standard 1 mm iso. The warping works fine - I am happy with the results visually. Then I applied the transormation to my tensor with the 'vecreg' command and I used fslmaths for tensor decomposition of the transformed tensor. There are strange lines outside of the brain along with some NaNs in the FA image. This does not occur when replacing the reference image with the original 1mm version! I found a post titled "odd behavior of vecreg" from June 11 2012 where Mark Jenkinson said not to worry if it's outside of the brain. fslmaths can of course remove the NaNs in the FA image but I am concerned that the V1 is also affected even inside the brain because the tractography results come out quite differently between 2mm and 1mm resamplings. Also, the 1mm results appear to be more similar to those in the native resoluton (2.5 isotropic). So I don't know if vecreg has also done something wrong with V1 in the 2mm resampling. Could someone help me to fix this problem, please? Thank you! Elisa ------------------------------------------------------------------ Saad Jbabdi, PhD MRC Career Development Fellow & University Research Lecturer FMRIB Centre, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK. tel (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi>